Before the patch I was in Level 3 of Crafting. After the patch its reset to Level 1. All other skill areas stayed the same that is the only one that reset back to level 1.
Log in directly through patcher once to see if it fixes. Bypass can cause these sync issues. A lot of times using patcher once is enough to get it working.
Do you box off the same installation folder? Need to narrow down the parameters of when this is happening to get data and reproducible steps for the devs.
I do have two accounts running off the same folder. Second account is fine. No reset on Crafting. Slightly worse. I just completed several crafting quests and the skill seems to be locked at 0% and will not go up. Other account still goes up on quest completion.
Just had the same thing happen on one of my accounts. Plundering was max lvl. Not it shows as lvl 1 no exp.
Try logging to desktop then log back in. It has to load up the Overseer data on demand after you are in world, if it fails it will do that and the only way to resync is to log all the way out. Your data is still there its just not being pulled down.