Those games are not  still quarantined.

Just ignore the delisting and update as you would normally do.

The thing is, any update (including the first upload) can get a game on a waiting list for manual review. And that includes a temporary delisting. Unfortunately, the waiting time on that waiting list can be long. Over a month sometimes. So you would typically wait a minute, a few days or several weeks. It is said, that this list is not first in first out.

And some random things can also get a game quarantined and for obvious reasons, Itch will keep those random things secret. There are real hacked accounts and malware out there. Based on my observations, there is about one hacked account with malware on the index every day. And if they take several weeks to remove reported malware, I have doubts that removing games from quarantine is any faster. R-107312 is now 8 weeks reported and still indexed. :-( 

If a game is quarantined it is also delisted, but there will be a quarantine message if you try to download it. (On the download page where to select the file)

For publishers the frustrating bit is, that Itch usually does not tell you anything about the status of a game. Is it intentionally delisted or is it still in the waiting queue? Was it "overlooked"? In combination of a waiting time of several weeks, much misunderstandings happen there. And Itch's stance about indexing is, you should not rely on it to begin with. There are reasons for doing it this way, but it still is frustrating for the publishers and at the places they would look for information (the faq), it states a waiting time of a few days, so people get nervous when nothing happens after two weeks.