It's difficult to discuss about a fix, since the problem is surely caused by something else. Clear proof of this, it's exactly that is fixed (randomly, and that's the key thing) by restarting Couatl, so the problem is likely either just memory (standard or VRAM) corruption, caused by too high settings AND/OR too many add-ons installed for that area, OR another product that is taking too much bandwidth for Simconnect commands, not giving a chance to our software to talk with FSX.
By restarting Couatl, you probably get a chance to let objects to be created while Simconnect was momentarily available and not too clobbered down by other add-ons. We had a similar issue with KDFW a while ago, when used to UT2 with too much traffic: those AI models were so many, that UT2 calling all of them in a short time, didn't left any time to other add-ons to talk with Simconnect, and this resulted in random missing or misplaced buildings.
That's just a guess, but it seems to be the most likely, according to your report. If the scenery or your installation had any kind of problem, you wouldn't see any buildings OR, by restarting Couatl, you would always see the same buildings missing, over and over.