Another approach short of rewriting all the scripts from scratch (probably not a practical approach for you) would be to write tests for the scripts.

That way, you will understand what they do, and you will be in a position where you can change/patch/fix them without nightmares of production stopping at midnight.

This approach has the added advantage that it looks very professional to outsiders (what rewriting typically does not do). And in fact, it is professional to do it like that. It will be a lot of work, though.

Update: chromatic reminded me to point out that well-written tests can serve as or aid specification and documentation. Yes, this is certainly true. Thanks, chromatic!

Christian Lemburg
Brainbench MVP for Perl
http://www.brainbench.com