Can only second this, in my niche, variations on colour is very common, and they really should be listed as separate items. I know some other systems that link into AE have this already, it's essential to fleshing out the store quickly.
Problem returned for me again tonight, this time with everything logged in as it should be. I do think it may have been interrupted half way, are prices set to $0 before being updated with the new price perhaps and so if that update doesn't happen it is left at $0? Still an issue there somewhere.
For me, I had to re-login to AliExpress in a separate tab, then run the manual update again and things seemed to be back up and running. I have turned off the automatic update for now just in case this happens while I am asleep.
If your session has logged out at AliExpress and you don't realise it before running a manual update of prices, every product that is processed has it's price set to $0.
If you are not watching, this means you have an entire store that is free!
Would be better to skip the update if the...