I'm running into the same issue. I downloaded a bunch of itch games through my browser, only for them to not show up after a scan.
It appears that games installed through the Itch client have a "receipt.json" file, which singlehandedly handles game recognition for the client. Also, dragging the receipt of game A (downloaded through the Itch client) into the install folder of game B (not downloaded through the client) and then scanning the directory causes game B to show up as A.
Perhaps making each games individual receipt file available for download could save all the hassle. After all, we could just drag the receipts into their respecive game folders and be done with it, instead of having to download the whole thing again.