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Nah don't worry. But having in consideration I can't help you cause I don't really understand: Check this gameplay and how he access to the Chapter 2 

Minute 22:02 (When he's on the Fake Computer, just reopen the emulator "isaac_beta02.exe" and select the chapter he wanna play. Its the same with every chapter.

So I think I understand the problem now, after I make people their Fursona and make one 'human', once the game closes and I reopen it, I don't get taken to the Emulator. Just Fursona Maker 3 allover again as if it was my first time opening the game