The most likely is that she'll wake up as if its the start of it all, in her Baby Finches personality, with no memory of anything that has tranpsired since the time loop began -- essentially an inverse of how the game started. the rest of the game will be Sensei helping her remember who she is, possibly through several resets, inverting their respective roles form the beginning of the game.
And I suspect the true ending at the end of it all will be this Sensei becoming lost once again, a season or two after Maya finds herself again.
They are, after all, Vega and Altair, ships passing in the night, only allowed to be together for the briefest of intervals before being separated by the sea of stars once again.