I do not really have any steps to reproduce this. This is happening in my modded SP Testlive.
This what I had in place when i logged out yesterday after replacing it the first time. Please note that the Set Brazairs are also disappearing. I was testing my thralls attack response in this area for another thread.
This is what I came back to this morning. yes, all of them returned to the general locations they were posted in.
Edit #1. Unloaded my mods and this is what i found so far.
So I took a walk around the area and found that about 12 of the T3 foundations are visually there, but support nothing.
Edit #2 I replaced (upgraded) the trouble some foundations with Aquilonian Foundations and the sanctum remained in place.
Edit #3 this is what it looks like after I replaced the ghost foundations.