Same for me but only the dyes are lost. Multiple relogging and restarting didn't help. Hmm not sure about the skins though...

I have a feeling the tracking system for unlocks doesn't work at all. I've picked up several of the same items and unlocked the skin every time.

Dyes, I have no idea what is going on here, no mouse over tooltip makes it hard to see if I am using duplicate items, or if the system isn't unlocking new dyes.