I created a new Switch account the other day now that cross save is live. I finished The Awakening that night, and then last night I linked the switch account to my PC account and obviously kept the PC account with all my progression. I played a single mission on Switch (the first one in Hidden Messages, if that helps with tracking down the reason) and then called it a night.
I logged in today and I had apparently lost progression on at least three of my unfinished achievements (Cryptographer, Field Medic, and Cheater of Death) in the client, but kept them in Steam. After taking screenshots of both sets of achievements to send in if it was permanent, I exited the game and logged back in, which returned the progression in-game as well.
So basically: if you made a new account after the merge cutoff, progressed the bare minimum, and then linked them, then apparently lost progression in some achievements in your PC main account, restart your client to see if it fixes itself!