I thankfully also always keep the latest zip so I didn't need to redownload the whole thing. The strange thing is when I started the game completly without mods I got an error loading the specific save before the Mira decision. When I only put scrappys mod I could load that save and I got the choice for Mira. So it worked with only the scrappy mod.
I downloaded scrappy's mod and looked at it. It's replacing all the episode_
x.rpy (1-13) files, as well as the screens.rpy and gui.rpy files. Other than the renders and audio, those rpy files are the guts of the game code. So it's entirely possible that something didn't work properly during an install/upgrade.
If you extract the game, mod it, then apply just the game update patch, then try to update the mod, things may get corrupted.
If things break unexpectedly, revert back to a known good (base version from the dev) and then if working, progress from there.