Renpy will pick up the saves, but it remembers them as "which line in the code were you at", which causes problems with updates: when there are small ones your saves can slide back and forth along a branch by a few posts. If there's a large new branch added or if there's a commented out section that got deleted (Angela frequently leaves those: writing a draft, commenting it out, and then writing the full version in between the draft lines, then at a later update deleting the leftover draft comments), then your save can jump from one branch to another completely different one.
My recommendation is, after you've seen every branch that previously existed and you've just downloaded the latest update, go into your settings (inside the penlight menu) and turn on "skip unread text". Then you can use the skip function to jump to choices until you get to the branch you are looking for from the beginning of the game. There aren't *that* many choices, so it's pretty fast.
The reason you'd want to skip unread stuff to get to unread stuff is that she frequently updates early portions one or two lines at a time, subtle tweaks and expression changes stuff. If you leave it to default (only skipping stuff you've already seen) you can't skip any scene because the game keeps going "Oh, you may have seen Hiroko say 'Back off asshole!', but you haven't seen her say 'Back off {w=0.5}{vpunch = 0.5}ASSHOLE!'" every 3 or so lines.