Hi Kevino, PlusSpec automates the input of IFC classification to the model which does help in Revit as you have items classified in Revit, yet if your crew is trying to edit the geometry you may find a similar issue to the one you explain. I am not sure why anyone would use Revit to do a bill of quantities? I could suggest that the team move over to Layout as you will have a direct correlation between your 3D model and the 2D documentation.
Have you tried using Layout in your workflow? Revit has its place in the market, however, most of our users, who used to use Revit say that Revit is overkill for residential design and construction, you get very limited output for the builder and structural lightweight framing is non-existent? PlusSpec and Revit are two vastly different animals, I used it briefly way back when, but the truth was I did not have the patience or time to be good at it. I am told that it takes 9 months full time to be considered an intermediate Revit user, creating families for Revit is something that many simply do not master and this is where Sketchup with Plusspec excels. I hope it helps.
There are workarounds yet I would need to know more about the type of work you are doing.