That's why you make a new version every day. Sometimes more than one per day. I've got hundreds of old versions, and I've needed to use them a few times. Using this method, if the .cap gets messed up, it's only a day's lost work. Hard drive space is plentiful and cheap - use it.
Making an RPG in CC myself though, I really, really recommend you use C2. Faster compile times, easier code reusability, more platforms to export to, less bugs and quirks to work around, better workflow, and by the time you manage to finish it, there's a good chance a native EXE exporter will have been out for a while since RPGs take so long to make. If scirra doesn't make a native EXE exporter, someone else will.