I solved a similar problem recently. I would suggest looking into the RewriteMap directive and using an 'External Rewriting Program'.
There are some big limitations with RewriteRule in terms of maintainability and robustness. If you haven't gotten there yet you may eventually. Only simple rewriting rules can be written safely.
With a rewriteMap you can create a php or perl script, take advantage of your existing code base, and perform all the rewriting rules from a localized place in your code which easily sits in version control.
I believe you need access to the httpd.conf (or vhost) configuration file though, RewriteMaps (or some related directive) cannot be put in .htaccess files.