One thing you could try is to set those files immutable using the chattr command. You would be unable to remove (or alter in any way) the file until you unset this tag.
This will ignore anything in /boot or /bin, but anything in there should be owned by root anyway. Before you execute that command, you should be sure you're getting what you want, so try:
find /[!b]* ! -user root -a ! -group root -exec ls -l {} \;
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