I think that in itch.io, the servers that host certain games suffered some damage or failure, or algorithmically delete games that have been without traffic for at least a year (Leafo confirmed to me that the latter is not how it works on itch.io). It could be one of the two cases that happened to you.
Viewing post in Oops! All games deleted.
Was that stated somewhere, this deletion mechanism? The game counter is rising steadily. If they would delete old games that no one ever visits, the game counter would reach some sort of equilibrium.
If you encountered missing games, there are lots of games that dissappear for various reasons. The two main cases I encountered are either it was malware/pirated and staff finally got a report and acted upon it, or more common, the developer has a weird and dumb update scheme were they redo the game page, instead of updating it. I lost games from my collections this way and had no clue what was missing and why, till I encountered the game again - with a higher version number.
They do optimise their search algorithm and what you get as a result for a search term is rather random with a grain of secret algorithm magic. So one day your favorite game might show up and the next day it might not.