I don't know how up to date it is but swtorista has a codex page and it has information on which ones are not obtainable. https://swtorista.com/codex/

Will we still be able to turn in underworld syndicate plans or use rep tokens after it ends?

This might be related to the keybinding issue? Quickbar 5 seems to be mislabeled as 4 and Quickbar 6 mislabeled as 5. When using the default interface and clicking the up arrow the numbers will show 1 > 2 > 3 > 4 > 4 > 5. The keybinding screen seems to have the correct labels though.

Checked again today and there were multiple panels available in the area. Was able to complete it on two characters.

This still seems to be an issue. Tried changing to PVP instance and re-logging but still not there.

Tried buying a belt from the tech parts vendor on the fleet with my Telekinetics Sage but I didn't receive anything. Parts appeared to be removed. Other pieces of gear seemed to work fine.

It was after Gemini Deception.

I don't know if anyone ever figured out the cause but Scorpio did eventually show up in my Consular's companions list after completing one of the later chapters.

Here is another one: http://www.swtor.com/user/ce/9rws

Not quite but Keith tried to reproduce it: http://www.swtor.com/community/showthread.php?p=9400153#edit9400153 Edit: Just realized that was a reply to you, so you probably already knew that and were looking for something older.

Didn't even go near the mobs. Picked daily up from the terminal, stayed near mission terminals a couple minutes then ported to stronghold.

I had picked up the mission [DAILY] The Dread Guard from the terminal but soon after traveled to my stronghold (had not gone to the mission area yet). When I got there the bonus immediately showed up and advanced to Stage 2. Remembered this bug so I checked my alignment and it had been reset. Also had Long Shots in my log. Maybe the bug is triggered by leaving when you have this mission in your log and the bonus not being complete?

This happened to my Trooper when I traveled to my Stronghold. I had Long Shots and the mission that has the staged bonus in my log at the time.

Always thought it would be kind of cool to have my other characters as companions. Could kind of build your own that way.

GSI Satellite Support lore entry is obtainable again. 5.2.1 brought the terminals back.