On the other hand, simply building nuclear weapons under all of the physical locations (or having self destruct back-doors built into fusion plants that were the local power support inside said locations) would get rid of the evidence.
Think about Firebrands conclusion of what was the Gamma Center site. That was demolition on a massive scale which -other than it looked like demolition to an experienced and trained eye- removed ALL the evidence of what had been there.
This is a ceramicrete civilization and unless you went out of our way to build with lesser materials, you are leaving shells that are really tough to change without ripping them down. What was in those locations? We don't know except for Albrect's private island compound which had to have been a really sophisticated base and communications center with all sorts of records and equipment. How do you rip that down- quietly- in what is supposed to be a nature preserve?
Mesa as scheduled to take the fall and essentialy reap the rewards of it's centuries long genetic slave business and I suppose that was supposed to be part of the cover to getting rid of a lot of physical evidence. Perhaps there was a plan-not implimented yet- to forment a Seccie/slave revolt which would end up wrecking Mesa and all those locations would have been "tidied up" as nominally many over reactions of the Mesa security forces. Look at how massive the Alighment presence was in keeping tabs on the Seccie population.
Just saying
