It turned out we had a few extra Lucida fonts installed as system fonts and it caused a conflict with user fonts that were Lucida as well, but slightly different one.
Do you use Lucida in any of your web-to-print templates?
If yes, you need to upload your Lucida fonts, please or let us know this font removal caused you grief.
Sorry about it. We probably did a bad thing that will affect a few templates. We want to know if it did.