Don't know if this is because of something you did or an itch bug, but with this update, none of my saves transferred and I had to copy them over manually. (I'm using the itch client.)
Viewing post in Weekly Update: v0.17.3! comments
For some reason Itch hates transferring manual save files on Android. Even weirder, it DOES transfer the autosaves (click on the "A" next to the page numbers on the load screen). The game autosaves every night so you shouldn't lose any progress if you sleep right before updating. Sorry for the inconvenience!