Okay so I haven't posted anything in about 2 years but ssshhh...
Apologies if anyone has already posted this theory, but the 'our loki will be with our Mobius' line from the featurete has reminded me of this. I don't think the Mobius we see at the end of S1 is from an alternative universe. I think it is still 'our Mobius'. Instead, Mobius doesn't recognise Loki because Loki has never existed.
Now Sylvie has killed He Who Remains, she is in control of the timeline. She uses her new power to give herself what she's always wanted: a life. To do this, she must first remove the existing life the Sacred Loki lives and replace it with her own. Two Lokis existing at once would probably cause too many nexus events for time to flow smoothly. Instead, Sylvie replaces Sacred Loki's life with her own, mundane one. This is why she works at McDonald's so she can live a normal life.
Loki, therefore doesn't exist, especially not in any significance for the TVA to take nite which is why Mobius doesn't recognise our Loki.
I think the climax of the series will be Mobius in trying to restore Loki back into the timeline by wearing the temperal radiation suit and physically repairing the timeline... risking his life to do so.
However, I think by removing Loki from the timeline, the timeline as a whole will begin to unravel. Without Loki, Thor remains an arrogant prince and never becomes a hero. The Avengers never assembled to stop Loki in New York. Thanos easily wipes out the half universe. This makes it even easier for Kang to take control of time with no opposition to stop him.
And loki will see that, even though he mainly played the role of villain on the timeline, he was just as vital as any of the heroes.