Obviously going to paste this into my own topic aswell, but I figured it is worth it's own topic to warn people who might not want to read through my massive list. Searching I can't find it being reported but if it was, do tell.

Later in the game, you get the option to remove your Source Collar. Upon doing this the guards start a conversation with you about your lacking collar. If you pick any option going to jail you go to jail. So far all good. You can retrieve all your items and move on.
It gets messy however if you talk to them again and pick the same option of jail. This time around, all your loot will be gone except for your equipped items and a few very specific items. I had however lost 98% of my equipment as result... RELOAD.
Pretty big issue, and can send you back a lot of time if you haven't a savegame in the vicinity.