Sorry for the lack of blog entries in so long. I've been busy working on the next CFWebstore release and doing a LOT of store upgrades for various people. Recently did an upgrade for an old version 4 site that had a lot of custom code and was able to cleanly migrate all the products, orders, customer accounts, etc. so it can indeed be done!
Previously I did an article on doing CFWebstore updates with ExamDiff Pro. I've since switched to a file comparison tool that is even better, Beyond Compare. It has some very useful features like remote file comparison and sync over FTP, manual line matching, ability to save sessions, etc. You can download a trial version and if you are already using another file comparison tool, drop them an email and ask about a competitive upgrade!
Beyond Compare also allows you to create your own color-coding profiles, here's one I created for ColdFusion users: ColdFusion BC File Format Import File. After importing this File Format, go into your Options and set the Display colors under File Views for the ColdFusion tags and functions.