I have had the same problem for months. Good luck on getting this solved. I had to remove SOS2, despite really loving my colony and the mod.

Thank you, still hoping for a solution. For a moment, I thought it would be you :-D

Same problem here. Built a new big cruiser (with mass over 5000), floored it. Sudden combat caused me to "move wreck" away, which moved ship away. About 1/3 of floors randomly disappeared from it. Brought it back after combat at the same place and found out that floors are "still here", except they're invisible and I can't move cruiser around at all - simply refuses to move either by salvage bays or RCS thrusters.

The only temporal solution I've found for now - explore planetary area to land all the ships, then use Blueprints mod in god-mode to copy-paste whatever ship is broken down to surface, delete space map (with old ship) and launch new ship from surface.

This also fixes issue with permanent "ship movement" tile blockers that appear randomly by moving ships around.

Can someone please clarify if this is still an issue?

Haven't seen a fix for it yet.

This problem disappeared for me by disabling the LightsOut mod

It's impossible to say what mod might cause this. It could just be a user's sorting order (SOS needs to be higher in the list) or it could be a mod that makes dirty edits, could be an error caused by another mod being removed from the list and then loading that save, could be a mod that tries to make removing an item impossible -- the best I can say is check your mod list for items on the interop list, and keep your load order clean and organized.

Vanilla + SOS2 never has this issue. It's always a mod trying to do something with storage of items, or requiring special handling when minified, destroyed, or moved. Which could be a whole range of mods that do that for any number of reasons.