Is it possible that mod_perl was upgraded, but apache was never restarted, and now that the machine has been restarted, mod_perl (the new version) ended up being reloaded? Perhaps your modules directory path was changed in your Apache configuration. Perhaps the system startup script points to a different version of Apache or module directory. The number of items that may have changed is pretty large. The node pointed to be vinoth.ree (below) sounds pretty close to what you are describing.
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