I think it was known that when an SACU is actively assisting a structure, it will auto rebuilt it when it is destroyed, regardless of whether
-The building belongs to the different faction as the sACU
-The building is unabled to be built directly. (eg ED2-ED5 cybran shields, upgraded eng stations, HQ factories)
When the rebuilt is done on upgraded hives though, the resulting structure is kind of messed up.
*Edit* I found the github issue reporting this, https://github.com/FAForever/fa/issues/553