Thank you for the report. I am sorry you are having a desync. This is very bizzarre. Could you include more details on exactly what you were doing at the time of the desync?
Also, it is impossible for machine upgrades to desync by itself (or even just with Rubia). This almost certainly requires another mod (in addition to Rubia) being installed at the same time. I am suspicious that this has to do with one of the many other mods being installed at the same time.
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I poked around your save file, and got more details from your forum post. I do not know any system on Rubia that would even touch the logistic network view you mentioned. Unfortunately, I would need to get together a MP party to actually recreate this and even confirm if it is actually Rubiaās fault. This is going to take me potentially days to find someone to properly test with, and coordinate.
Since you have a very large number of mods on this save file, would you potentially see if you can reproduce this bug with only Rubia installed?
What I can tell you is that it is highly unlikely that Machine Upgrades causes this desync, as it doesnāt interface with any logi-nets or logistic UI. Rubia at least listens to UI changes, but the behavior on all the modern versions of Rubia donāt touch logistic connectivity iirc.