Well, I got another BSP related bug today, which is beyond frustrating. Basically, my project is at a point where if I click Build All, Build geometry or build light, then almost all BSPs either disappear (ca. 90 % of them) or are incomplete. And so far I was not able to go around it. The only way seems to give up ALL BSPs and replace them with static meshes.
I googled it and this bug was around many ue4 releases ago but I did not find any actual solution (except deleting all brushes). It seems that 4.13 makes many BSP related issues much more likely to appear than in 4.12 (this is 3rd major issue I had with this single project) but I cannot convert to 4.12 so it is hard to judge.