the safest way to go about retroarch updates is to backup savefiles, savedata and system folders (potentially also remaps), then deleting the entire retroarch folder and putting the new one on the sd card, then copying your backups to the appropriate places.
since it speeds up startup times significantly, you should then delete all the cores that you don't use and the info files for them too.
and finally, yes, install those core cia files with fbi.
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Anyone knows why I only get crashes (both arm crashes and crashes that send me back to home menu when trying to run ps1 games?
I've got bios files, I'm using a nightly from one or two days ago, I'm using games in pbp format that work for my ps vita.
I've also removed config files to make new ones in case something was wrong with that.