If you go into Operator-mode (War Within's version) while you're extracting in a mission, you lose all in-mission Syndicate XP gained. I tested this a few times (when I had daily Standings still available) and it worked each time. I haven't tried in the latest hotfix, but I don't see any patch notes on it, so I assume it isn't.
This bug applies only for Syndicate gained from wearing a regalia. It does not affect standing reward from Syndicate missions nor does it affect Simaris' standings.