Hey, if you want you can reach out to me on discord and I might be able to help out in a little more detail. Its easy for me to lose track of messages on here.
Discord: #mr01sam
So, it sounds like the main issue is that Heli's are destroying surface foundations, which in turn, is destroying the basements. Basements shouldn't have any affect on changing the heli's ability to hurt surface foundations, TruePVE should be handling things like that.
If you don't want basements to be destroyed when a surface foundation is destroyed, there is a config setting for that. Assign "Destroy Basement Cell When Surface Foundation is Destroyed" to "false" and basements will only be destroyed if all entrances are destroyed.
I hope that might be helpful? If not, feel free to reach out on discord.