I see that the other thread got closed but my custom domains are not back.
Glitch staff are working with Fly to get this 100% fixed, this should be solved by the end of the week (I hope)
As @RiversideRocks stated, fly has made a temporary fix. We will be discussing a longterm solution with them this week.
In case anyone else is still having trouble, it turns out you need to have the folks at email@example.com clear your domains and re-add them.