I have a similar problem with Battlestar Galactica Deadlock: Modern Ships Pack DLC. I got the Modern Ships Pack for free with the
Armistice DLC launch promo back in September. I noticed the disappearance on Dec 12 when I was downloading the latest 1.5.112 installers. I had downloaded the installer for the previous version 1.5.111, which according to gogdb was added to gog on Nov 4, so the disappearance must have happened sometime between those dates. Modern Ships Pack is also not marked as owned for me on the store listing or gamecard. All other Battlestar Galactica DLC are still listed in my library and marked as owned on the store listing and gamecards.
I made a support ticket about this on Dec 12 and got the autoreply, and the next day I got an email stating that my ticket "is currently being processed, and one of us will get back to you as soon as possible." After that, nothing, and the DLC has not returned to my library.