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I headcanon that when Morgana tore the veil between worlds (s4 e1), she created an alternate universe. Meaning that all the events that took place afterwards happen in a different/ parallel world to the one before.

It is based on this quote,

You are right to be afraid, Morgana. Your enemies will rue this day and all the destruction it brings, but you must beware. Tearing the veil between the worlds has created a new world , and you will not walk through it alone. The one they call Emrys will walk in your shadow. He is your destiny, and he is your doom.

- The Cailleach, Season 4, Episode 1: The Darkest Hour 

From this, I think its possible that tearing the veil was such powerful magic that it changed the destined/ predetermined future, erased past events and altered the very geography of the world.

Here's a quick list of some of the things that I think could be attributed to an alternate universe, 

Changes to Destiny / Predetermined Future

Morgana and Merlin's have new destinies

The Cailleach specifically warns Morgana that Emrys (Merlin) “will walk” in her shadow, indicating that wasn’t either of their destiny beforehand. Merlin no longer has a destiny independent of Morgana. He has to walk in her shadow and cannot be anything but a figure of Morgana's destiny.

The Cailleach also says Emrys' (Merlin) is Morgana's destiny and her doom. The Cailleach isn't as specific about when this became true, but I like to assume that he wasn't before. That before the veil tear there was a chance for reconciliation.

Morgana even gets a new prophecy - to bring back the Old Ways. Pretty sure the first (and only) mention of this is by the Dochraid in the Lancelot du Lac episode. In the earlier seasons, her magic isn't that powerful or strong. She admits it herself, so does Morgause, the dragon scoffs at the thought of her using a crystal. Post tear, Morgana has a lot of power and is suddenly a high priestess having had very little formal training.

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When Merlin and Morgana's Destiny change, this has knock on effects for everyone else.

Albion now has a new darkest hour: In the old world, this was the Immortal Army attacks at the end of season 3 (s3e12 & 13: The Coming of Arthur). In the new world, it is the tearing of the veil/release of the Dorocha. (I do not recommend binge watching season 3 into 4, you don't have time to recover from the last darkest hour before you're straight into the next, anyway). The change in the darkest hour, once again alters Merlin and Arthurs destinies.

Post tear, the destiny of Albion gets rather confused: I'm pretty much with it until the immortal army darkest hour. The land is in ruins and divided between people who supported Morgana's short reign and families of those slaughtered with magic who possibly want a second purge. This could be a great place for Arthur and Merlin to offer a secret third option... but in s4 & 5 the destiny of Albion gets confusing for me...

It could be because Merlin's destiny is now to walk in Morgana's shadow, the old world prophecies are somewhat obsolete.

Changes to the Past and Geography

The events in The Nightmare Begins Episode are erased from history: It's like that episode stopped being canon. The attack on the druid camp appears to have been forgotten in the A Herald of a New Age episode and by Mordred when he returns. 

The heart of the Old Religion moves: According to Gaius, the Isle of the Blessed was the focus of the Old Religion’s powers. (S1:E13. Le Morte d’Arthur). After the new world, both Gaius and the Disir said that the Caerlanrigh was the heart of the Old Religion and the centre of its powers (S5:E6. The Disir). Also the Disir have the power to judge and destroy Arthur in a way they didn't do to Uther.

An entire mountain range moves: The Wilddeoren infested Mountains and Tunnels of Andor were located North East of Camelot on the border with Mercia (S2. Lancelot and Guinevere). After the new world, they are located South West, between Camelot Citadel and the Isle of the Blessed (s4e2: The Darkest Hour). Merlin doesn't notice why the Isle of the Blessed looked different or why it took extra time to get there.

Now, I’m all for a magical world but this was super random... unless it is a physically different world. Tearing the veil created a new world. Literally. It created a whole new one with new geography.

There are probably other changes that could be explained by a parallel universe theory (and likely a few that can't and are just regular plot holes). This is what I've thought of so far and I might add to later. But, I think there's enough changes to entertain the possibility that events post-tear happened in an Alternate Universe.

This then creates another question - what could have happened if Morgana didn't tear the veil and the original world/destiny/timeline continued?

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The way I see the show is that seasons 1 & 2 were the set up and season 3 was a transition. It wrapped up the early part of the show and set up potential for several different plotlines.

Uther had been questioning his harsh stance on magic since his mandrake root poisoning. Merlin, Arthur, Morgana and Gwen were all pushing the boundaries of their status and, especially in the case Morgana, making some decisions which had significant consequences. At the end of the series, Camelot faced its darkest hour - the invasion of the Immortal Army (s3e12). Merlin was reunited with Freya in Avalon and, against the odds, Arthur triumphed - a better world is in sight.

Series 4 opens with preparations for the feast of Samhain, Merlin is happily running about the castle and the knights have settled in, Arthur is prince regent and pretty much the de facto king and getting advice from his new creepy uncle, Gwen is finding a new place in the castle now she's not Morgana's maidservant, Morgana is questioning Morgause's plans on a partially renovated Isle of the Blessed.

No veil tear means The darkest hour stays as the Immortal Army invasion from The Coming of Arthur (s3e12 & 13). 

"When I met the Fisher King, he gave me this. He told me, in Camelot's darkest hour, when all seems lost, it would show me the way."

-Merlin to Gaius about the Immortal Army invasion and the Avalon Vial (The Coming of Arthur)

In the 'old world', Cenred/Morgause's Immortal Army invasion was The darkest hour. Merlin and Arthur's destinies used to be heavily linked to this event. However, the 'new world' (post veil-tear) the dorocha attack is The darkest hour. So, the Immortal Army invasion isn't the turning point it once was.

Without the veil tear/dorocha darkest hour, the Immortal Army darkest hour would remain The one and only darkest hour. It could be a Major Event that had wide reaching effects across the land. Rather than being something confined to the two episodes.

It was really quite the devastating time. The entire army from Cenred's kingdom was killed in one day! Then there's the villages destroyed on the march to Camelot (there's a deleted scene where one of these is Percival's village) and the Camelot citizens that Morgana slaughtered. The land is in ruins and its people broken. From this, Arthur could emerge as the king to rebuild and create a different/ better world.

Similar to the Great Purge, it could be an event that characters remember (it could even get a cool name - Dark Days? immortal slaughter? Immortal invasion? Whatever). There's potential for actions to have consequences.

Some characters might want revenge for their loss. Others might have supported Morgana's short reign. Perhaps Morgana wonders if she did the right thing?

Morgana could reflect on her actions during her reign. Either facing them or ignoring them, defiantly believing in her own self-righteousness. Morgana is so like Uther in many ways. There could be more of a parallel between the Great Purge and the Immortal Occupation. Both of them believed they're actions were justified - defending the people against terror and fear, but somewhere along the lines both of them became the very thing that they were fighting against.

This is something that I think Uther realised when Morgana told him and that's why he hasn't recovered.

Changing Attitudes towards Magic

I think Uther was becoming less harsh towards magic ever since his poisoning with the mandrake root (s3e1). There were fewer raids and executions than in seasons 1 & 2, he suggested using magic to heal Morgana (s3e6?) then Morgana's betrayal left him near catatonic with grief. 

Arthur's views on magic are also conflicted. He doesn't think all those who use magic are evil, but nor has he seen many instances of 'good' or even neutral magic being used. I think it would be cool to see Arthur and Uther having a chat about magic and how neither of them actually know much about it. It doesn't have to be a long chat, but just something that could pave the way for Arthur to have Thoughts about creating a fair and just land for all. 

Arthur expressed his admiration for the Ancient Kings and their values of equality (s3e13). These people had a seat for magic at their table. (Yes, I know this was an artist's choice to give a seat to each modern character. But canonically, this makes no sense.) In later seasons, Arthur brings back the round table, but not the magic. It could be interesting to explore more about the Ancient Kings and how they regarded magic. This would provide an alternate option to either Uther's regime or the High Priestesses'.

The future isn't set in stone, there are many paths.

Up until the veil tear, I feel like prophecies were shown to be rather more vague and difficult to interpret. As an audience, we saw many of Morgana's visions which were flashes of scenes but rarely played out as expected.

Merlin, on the other hand, had never seen visions before the crystal cave so he has no concept of what Kilgharrah might be basing his prophecies on. Since then, he has also witnessed the Fisher King's prophecy come true in a pretty convoluted way. Merlin now has a lot more knowledge about prophecies and destiny not being all that they seem.

Kilgharrah's prophecy that Merlin must protect Arthur until he is king is a bit vague especially when he tacks on 'only then will I be free' (end of season 1 I think) since Kilgharrah was physically freed during Uther's reign and we're not shown any other freedoms of his when Arthur becomes King.

I wonder if Kilgharah's prophecies were like Morgana's in that they were just flashes of events and, much like Morgana, he misinterpreted them. (Possibly, that's also why he went on such a rampage in The Last Dragonlord).

In the early series, Merlin frequently questions his destiny and after season 3, he knows more about prophecies but somehow questions his destiny less. Instead, Merlin could question what Kilgharrah is actually basing his prophecy on and learn more about the things that are written about him.

Merlin could maybe chat with Freya again. They were reconnected through the waters of Avalon. It's possible that they still chat and Merlin could have another friend who possibly has better knowledge of prophecies than Kilgharrah. Or with Gaius who thinks there are many futures.

Or… decide to ignore it completely and just live and learn like Kilgharrah told the audience Merlin must do in the very first episode.