Thats because Ch1. and Ch2. shares the same save folder: \AppData\Roaming\RenPy\Milfylicious-1668113355
I made a small "hack", I've opened the Ch2 v0.29's options.rpy file, search the define config.save_directory line, and change Milfylicious-1668113355 to MilfyliciousCh2-1668113355 and save the file. So, from now I have a save directory for Ch1, and a different one for Ch2.
Problem with that, every time when a new update released, I have to change that line in the options.rpy, or overwrite with my modified one before start new version.