https://bugs.winehq.org/show_bug.cgi?id=53046
--- Comment #4 from Rafał Mużyło galtgendo@o2.pl ---
You don't want to do that. AFAIK upgrading existing prefixes two years worth of versions forward is not going to work.
I'm not 100% sure, but I feel you're wrong here. Those messages look more like an *improper* update.
Would OP elaborate on how exactly they've updated wine ? Was it by using their distro package ? Did they *fully* uninstall the old version, so that wineboot couldn't get confused by old lib versions ? For the most part, if rerunning 'wineboot -u' alone doesn't help, manually cleaning prefix' system/system32 dirs and 'wineboot -u' should (in most cases).