My count is down by one as well. I no longer have the game "Penumbra - Requiem" (1207662753) in my library, however it seems that the game instead appears as a "DLC Download" under "Penumbra - Black Plague" (1207662743).
Curiously, both of those IDs appear when I visit https://www.gog.com/user/data/games
. Cross-checking the size of these installers with MaGog's cached info also seems to indicate that this is simply a bundling of the games.
I just checked penumbra_black_plague with gogrepo.py.
Those files that were in penumbra_requiem are unchanged.
GOG just moved all of them to penumbra_black_plague.
Those 6 zip files are in fact only 3.
PENUMBRA - REQUIEM GOODIES are just GAME GOODIES.