The feature is inconsistent and without consistency, it's difficult to pinpoint cause and effect.
I never used the bookmarks, or at least I haven't used them in nearly two decades. The current version has a nice feature where if you edit a route, then exit and edit the session you'll be put in exactly the same place where you left in the session. This is convenient for fiddling around such as adjusting sidings after finding them in the Session editor as I'm setting up consists. I don't use UDS unless I'm testing something such as signals or ATLS crossings and then I don't save anything unless I make a change in Surveyor.
The problem is, sometimes going in reverse from the Session back to the Route Trainz "remembers" a location somewhere else that was edited many hours or sometimes a day or two before.