Hi. What do you exactly mean by “stacked” BSPs. In my case I have a usual building/apartment scenery where BSPs are used for walls, floor, ceiling and some additional details such as doors or frames. So in order to avoid wall gaps, yes, BSPs are touching but they are not really stacked on each other. A wall is typically touching a floor, ceiling and adjacent wall(s)… and I still have the “losing material” issue.
Anyway, as I have just described in a comment above I am currently fighting with another BSP issue - when building geometry or lights, most of BSPs become invisible. It might be some kind of Order issue but so far I have no clue how to fix it. The only apparent solution seems to be to replace/remove all BSPs (50-100 pieces).
I am saving all maps with these issues (with this project 3 BSP issues) and so far they reappear when I load these maps so if you need a feedback in future, please let me know…