So I recently completed the 3.0.19 install enable to have the latest version and to then complete the 3.0.20 patch. However, stupid me forgot to copy all my mod files first and thus lost everything I had been working on when I did the install.
My suggestion though for going forward is that whenever the developers change an element within the mod kit that details of those changes are included in the patch/install notification. This way if perhaps a new field is being added to say the Product Type file, we will know exactly what changed and how we could integrate our previous mods into the new format.