I had not, and those 2 were the only ones that reset. I barely even paused let alone touched any settings. I feel like it may relate to when the money is ready to be collected given that it happened at end of the first month, which I think was a Monday as well and I believe it happened on a Monday the second time. I would've noticed before if it happened before then since I see that menu a lot since I frequently use the "Date" feature. I'm a wild guess could even be related to the level accidentally being messed with when backing out of a bad date location or gift when tight on money since I'm unsure how Ren'py handles the "back" button.
Don't think it's a back button problem. Hard to figure out what's going on and since you said it's no longer happening and this is the only report I got of it, I'll just ignore it for now. I did have a look into the code for anything that has to do with setting, adding, and subtracting the girl's levels but there's nothing there that resets it like that so I'm stumped in recreating it.