Grargar: There have been cases in the past that extras were removed from users' accounts. The Atlantis games, for example, had their soundtracks removed and in another case, Imperial Glory's Mac version was also removed, because GOG didn't have the rights to distribute the Mac version.
I can confirm this on some changes, like in Two Worlds 1 + 2, some extras went missing over the course of one or two years.
In addition, game compilations available on GOG are mostly based on the budget disc compilation releases of the time and thus had missing some of the extras of the individual games. After sifting through my USB HD archive, I did not find missing stuff, but I'll do it thoroughly after shopping in town :)