my experience with most renpy files is that you have to manually copy the saves over.
just like with RPGM
I honestly dislike how some renpy games save it in appdata as it makes a mess of version migrations
I've played over 150 renpy games and had to do that once... Just dont copy it next time and see if the saves show up in game, because I highly doubt that the games you play are all different from mine. Windows 10, older, or a different OS? Maybe you have a setting that clears appdata/local stuff? But one thing I know for sure is that that's not a renpy thing, ask anyone here.
And about the version migration stuff you mentioned... If an update breaks saves they should mention it, however if it does not break saves (which is the case often) this, as in saving in appdata, is the superior way. Which again is why its a renpy default. You want defaults to handle cases over 50% so it honestly makes sense.