Do you use server console to close the files before you reboot the server?
If not, you risk corrupting your files when you reboot. It's like a forced quit in FileMaker Pro. When the server re-opens the files after the reboot, it'll do a consistency check and then will fail to open the files if the consistency check discovers file damage. It's a roll of the dice each time you do this, you may have just been lucky before now or some latent file corruption has accumulated to a point where it now fails the consistency check each time this happens when it didn't before.