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Will show you any processes that have the file open. If a file is open by a process it shouldn't be deleted. In fact it never really is - only the name is - the inode stays active until the process that is holding it open goes away - like in a reboot.
Neither of those sound like critical system files so deleting them even with a running process shouldn't cause a crash.
It sounds as if you may be having a drive issue. Have you looked through /var/log/messages (messages.1, messages.2 etc...) at the time of the crash to see if any errors occurred at that point?
It might be worthwhile to reboot and run an fsck on the filesystem at boot. I wouldn't do that until I'd ruled out a drive issue though - it might make things worse. You may want to try backing up everything then doing it.