Organizing the rest of Sonar's files has always been a royal PITA because Cakewalk doesn't always make it clear which data is static, which changes, which is static but gets copied to be changed, which is per-program, which is per-user, etc. And those decisions seem pretty arbitrary - for example, Cakewalk dumps a load of copied drum maps into my user/appdata directory which I will never use (alongside the 1 or 2 that I do), but the project and track templates folders (which have far more documents that are personal to me and edited by me) are over in Cakewalk Content, which is mostly for static data. I don't know how much of this is due to my upgrade settings and how much are just inertia on their part, but it's very disorganised.
The most important thing is that you go into the Sonar preferences, check the myriad of folders listed there, and make sure everything that
you care about is in a directory that is getting backed up.