Originally posted by Jitatha:

Can you supply a screenshot? What you describe sounds fine, however there are some draw order issues in the game which can cause unexpected disassembly, or pets to escape etc. These are especially prevalent if you use "fly", but I do not think you are doing that.

Here is a link:
https://imgur.com/a/gJgGKOC

Destruction happens whenever I travel via portal or by foot away and back to base. No console commands.

I have to add I noticed strange behaviour of parts around these destroyed chests. When I rebuild them for a moment there were parts more than 1 block away from blue foundation parts and they were also marked blue. After few seconds they turn green. Tried to rebuild them too with no effect. Could be the draw order you mentioned.