Here's the official word on it:
"Hello, we have made a really huge investigation into the issue. First of all, I can reassure you that no game is missing from your library. We are still not sure what causes the problem, but we also know some of the conditions required for the problem to appear.
First of all, a user must have a large collection of games, at least over 70. Some of these should probably should be games with DLCs (the problem never happened on an account without DLCs, however adding these to an account will not trigger the bug, that's why we're treating it only as one potential condition).
The missing spot will always appear as the last entry in a row, usually (but not always) right down the middle of a library. In case of collections with at least 300 games, more than one empty spot may appear. The empty spot will always be in the same place, no matter what kind of sorting method is selected.
However, as I said previously, we are definitely sure that no game is missing and apparently it does nothing except being there. Because of that, the problem was unfortunately assigned a low priority, and will likely only be fixed only after more urgent or serious issues are resolved. This will probably be no sooner than 2 months from now.
In this situation, all that I can do is offer our sincere apologies for the issue. I hope that it will not be a huge inconvenience to you."
Looks like they're aware of it, though it supposedly isn't related to the Witcher Adventure Game Beta being removed. Nothing to do but wait.