And using Perl tidy I am able to generate 'tidy' looking web pages.

I can't understand. AFAIK Perl::Tidy is a tool to (mostly) beautify Perl source code. What does this have to do with "'tidy' looking web pages"? Aren't you perhaps confusing with HTML::Tidy?

But the code is in CVS. How can I make the POD abreast with any changes made in CVS?

In all earnestness I can't make sense of your question, but the most reasonable guess I can come up with is that you're concerned that minor changes to the text and passes through your reformatter will wildly change the source itself making for poorly identifiable diffs. In that case, there are better algorithms now than CVS's. But if that is not an option, reformat once and be careful about pod yourself. Or am I completely off base?