Same thing for me, I’ve been achievement farming on Remix with my Druid and I’ve had no prbs until TWW prepatch. Waited a day before I could play and when I finally got back on Wednesday (24hrs after patch), I hit exalted with Order of the Cloud Serpent and didn’t get the Remix achievement. Upon logging out of the game and back in (with no addons loaded), I got the original MOP OotCS achievement to pop, (which I didn’t have because I skipped the MOP exp in the past), but still didn’t get the Remix one. I only care about the Remix one as that’s been my goal for Remix the whole time is the achievements. Now I’m worried about continuing to pursue grinding for any of them. I hope Blizz can fix this soon. 
Edit to say: I did enter a bug report on the matter and opened a support ticket. Got a canned response though. “Check the forums for assistance.”