In my case I need to add the note that my game play is usually multiplayer (only 2 people total) so it might factor or might not.
When i had depots dissapear on me it was usually when neither player was around
Example it might have happend on a planet one of us was on, or a planet neither of us was on.
One I had recalled was.
I was on Nauvis and my friend was over on Fulgora.
after a few hours we noticed our platforms bringing in resources from Vulcanus to either of our planets was lacking or missing.
going over to Vulcanus we saw almost everything stopped because one of the primary depots for iron plate was just... gone..
neither of us had been on or interacted directly with vulcanus at that point for around 3-4 ingame hours.
in 1.0 days we would be in a save and after 100 hours or so we noticed 3 or 4 random depots we setup like 50hrs ago was just missing for some rason.
For additional context both times the game save probably had a few 100 (or even 1000+) trucks.. and 100's of depots.