achievements not granted?

[Sleepy Lich Disease]

despite finishing the entire game, i only have one achievement? for context, i finished the entire game before the first patch was released. after finishing and closing the game, steam notified me there was a patch. i launched it just now to see if loading my file would pop the achievements, and the only one that was granted was the one for connecting the pipes, and my save file was right before
posting Herbarium in the mail so i did that and got through the ending again, and was able to unlock that achievement but was still missing the rest. do i have to replay the entire game just to get the achievements that seem to have been missing on launch?