I've the same problem in one of my bases, single/local world: I flattened the terrain but, sometimes (didn't find the "triggering condition") it opens 1 m deep "hole" and I even can walk into it (so the physics is "preserved", the engine knows it as an hole, not flat terrain).
Only things I noticed are (1) items remained suspended over the hole seems not suffering the loss of support, not breaking/decaying, and (2) if I leave and get back (or even just after some time I'm there) the terrain gets back flat as usual.

First time I saw that effect I thought it was me, to make a mistake, maybe flattening/digging at night, when the 3D perspective is weak, so I re-flattened (raised) the terrain up... only to find a little "hill" later. :D
Since that moment I just ignored it, thinking it was a terrain-map's glitch.
I can confirm the problem lasts far before the last patch/update.