Have you tried rebooting yet? Apple made a rather silly mistake recently. and remotely shut off a bunch of people’s right to run certain programs. This problem has since been fixed, but you might have lingering traces of what caused it still on your local machine. If a reboot doesn’t solve it, I would take the advice of the error message and reinstall the software.
As for your files, this is just a problem with the software. In fact, it’s not even a problem with the software. It’s a problem with a piece of information on your computer that tells Apple you own Scrivener being out of date with what it is expecting.