Looks like desyncs was caused by turrent shields mod. Desyncs are happening right after marking turrents with shields for automatic deconstruction by bots. We removed this mod and issue resolved.

We played a map on a server with 3 players and (possibly) after placing a blueprint over items marked for deletion desync occured for all players. After reverting save file to most recent autosave, desync was not happen for a while, but after some period of time started to happen again periodicaly ...