Our mc has gone through so many loops now that nothing is going to make sense to her or us without a lot of guesswork. Unreliable narrarator type shit.
New villain and at the start might have some kind of close relationship with the false god. Or he's another human turned servant of it. Which means he has a certain amount of power to manipulate reality in the town. The other servant could turn people into flowers. So whenever mc gets her wish granted, he might be tweaking some shit here and there for entertainment. The other twin is alive in this loop. Why? This new antagonist we just met seems to like watching stories unfold before him. Who would want to read/watch the same thing on repeat forever? No one. I imagine he's technically stuck in the loop with them.
So the question isn't why is it a different twin this time. It's how much has this guy manipulated the multi-loop from the 1st time it started.
I imagine this also makes it harder for the mc to remember anything without it seeming like a dream. She just thought she was tweaking out when the wrong twin showed up in front of her. They could have a chance at retaining all of their memories if they can reach the new antagonist and kick his ass. That information could then be used for a final loop where they save as many people as possible and kill the false god.
TLDR: I presume the new antagonist has influence over the loop and treats it as a means of enetertainment. No two loops will be the same because no two episodes of a show are the same. No two books are the same. That would be boring writing which antagonist would hate. He's evil evil.