I realise this is just a few years late, but ...
I had the same problem happen to me on a route I had started creating in TANE SP3. This was before I knew the difference between editing a route vs editing a session and how the route and session layers worked in TANE. (I had migrated across from TRS2004, skipping all versions inbetween, so it had been a bit of a learning curve/adjustment coming over to TANE because of these differences)
After a year or so and a new pc, I have now reinstalled TANE and updated to SP4, loaded the route and some of my baseboards were missing!! All the scenery, track, industries etc were still there and visible, floating in midair. It seems that I had inadvertantly added these boards whilst editing the session and/or having the session layer selected in surveyour, rather than the route layer. (or at least that is what I think must have happened because if I edited the ROUTE, the boards AND the scenery etc were missing, but if I edited the SESSION, all the scenery etc was there, but ONLY the baseboards were missing... )
Anyway, I got my baseboards back by entering surveyour via the "edit session" option (selecting the route/ clicking "view sessions"/ selecting the session/ clicking "edit session") and then I merged the session layer into my route layer, saving it and overwriting the orginal route and session and then reloading it. (I would suggest perhaps renaming the route and session so you still have the original backup incase) When the route reloaded everything was back! As my baseboards had not yet been textured, I cannot say if this would retrieve the textures or not, but the boards that were missing are back. As you cannot change the layer to which the baseboards are in like you can for most other assets via the edit properties "question mark" tool, merging the layers seemed to be my only option..
As far as I can tell, the only difference that entering surveyour from the route page or the session page makes, is which layer is highlighted and selected for editing when surveyour opens.
Hopefully this solution can be of help to someone out there with the same problem. Just remember to make a backup or save it as a different name just incase...