I should have written "but can't be automated in your situation."
Technically, it can easily be automated with the Apache commands as pre/post hooks - but there are so many drawbacks/caveats involved with doing that to a production site running mod_perl apps compiled into the server, that no one should automate it as it can't be done reliably. You run the risk of extended downtime during the renewal or Apache not restarting correctly, so stuff like that really needs to be done manually.
Doing this at 4am for a vanilla Apache install on a sleepy website is not an issue. The OP is dealing with a mod_perl install on the server that handles homework submissions for a university - which means it requires relatively high availability.