Two people have pointed me to this thread regarding saves, so I'll chime in real quick and then peace out.
My Ren'Py port of the game Long Story Short (check my sig) also uses python classes. I've not received any reports of saves going bad since I released it about a year and a half ago, or so. I've had to modify the classes due to various reasons, whether to add new properties or remove something.
Using the Ren'Py after_load label allowed me to do so. An example:
Python:
# Changes to classes
if not hasattr(mc, "told_ann_blackmail"):
mc.told_ann_blackmail = False
if not hasattr(mc, "ann_late_gf"):
mc.ann_late_gf = False
if not hasattr(mc, "ann_late_hate"):
mc.ann_late_hate = False
if not hasattr(mc, "chris_status"):
mc.chris_status = ""
if not hasattr(mc, "mean"):
mc.mean = 0
You can also delete if you no longer need a particular property:
Python:
# Changes to classes
if hasattr(insta, "triggers"):
$ del insta.triggers
Hope this helps.