A new awesome bug has been introduced with patch 5.9 which resets your in progress achievements back to zero. It has been confirmed by multiple people and appears to be easily reproducible. Bioware have yet to respond. My recommendation is to screenshot or record your achievements in case it happens to you.
"This is a very serious issue and we're working on a resolution right now. The goal is to match up your achievements before the patch and merge them with the progress you made after 5.9.
Our plan is to have this resolved today for anyone impacted. It'll require us to bounce the servers (essentially take them offline for a short-period, make the change, and restart). Once we have those details, we'll add the downtime information to the SWTOR Launcher.
We have Game Update 5.9.1 scheduled for May 22, 2018 where will be addressing other issues you may have encountered with 5.9. "
#13761931 May 04, 2018 at 07:51 PM · Edited over 2 years ago
"Our plan is to have this resolved today for anyone impacted"
...3 hours later...
"Our priority focus is to resolve the issue related to the resetting of achievements. After that is deployed through a short downtime later today (it's being verified right now) and we know we've resolved the issue, we'll begin working on retrieving past achievement progress and, where possible (my disclaimer), add progress made since 5.9, for players who experienced this issue. You do not need to submit a Customer Service ticket!
Please note this will not be resolved and deployed until next week at the earliest, as we need adequate time to validate your data will be properly restored."
So after I ran that through google translate it sounds like they are restarting servers today to stop the problem happening to anyone else and that those already affected should have their achievements restored next week.
Personally, I am going to record myself going through all my achievements so I don't get stung by customer services later telling me they have no record of XYZ etc.