Solution, if u meet this as user:

If someone use this on Gleba and have desync everytime ur friend join ur game, remove all belt-balancers, which can interact with spoilable items, then let ur friend connect, and u can place them back.

Copied from opened issue on github:

Desync happens right in the moment, when friend finished downloading and trying to synchronize.
As theory, I think, items are all spoiled in internal storage causing problems, after I removed all belt-balancers used on Gleba, friend was able to join, after that I restored all balancers used on Gleba.

Download desync report: Google drive
Also in archive I included report from Hornwitser's Python Scripts (desync diff/.dat parse/multi instance)

upd: forgot to mark thread as bug ._.