Here's a hint. Don't know what it means.
In regards to wondering if you have a backup? From the text following that, I would presume "yes".
I don't use any type of remote storage, though an iCloud Drive isn't quite the same thing. It's a file sharing space. Anything you drop into the sharing folder can be accessed from any of your other devices. By creating copies of anything you put there to the cloud, it's also an ad-hoc backup system. However, I'm not thrilled with how it works, based on a description found on the web:
You can store documents, keep files and folders up-to-date across all your devices, work on items and access them from anywhere using iCloud Drive. Changes applied to a copy of a file on one device will automatically sync across all your other systems.
Hmm. So at one time, there could have been undamaged copies of the fonts on your system. But if they "change" in any way, iCloud will update the remote files to match. If you had good copies on the iCloud drive, now they're damaged copies, too. The site continued on with:
If you use iCloud Drive across multiple Macs then changes made to the Documents and Desktop files on both Macs will sync. The Mac you activate last will create its own folder for the contents of its Documents and Desktop, and this will also sync.
Also a possibility of losing good copies of files. If the last Mac to be activated had bad copies of the fonts on the drive, those will sync to iCloud, overwriting what might have been good copies. Your Mac in turn, pulls those damaged copies down to sync across all of your devices. Then, oh goody!, now you don't have undamaged copies anywhere.
This is one reason I will not use such systems. So, that brings me to what I meant by a backup. And that's, do you have copies of the original, and then likely undamaged fonts on a local, external drive? If so, pull copies of those fonts back to your Mac.
If not, your only way of replacing them is to go back to where you purchased each font and download clean copies from them. Normally (with most vendors), once purchased, you can always login to your account and re-download those items.
I moved the fonts from Font Squirrel from the desktop folder, which is in the cloud, to the Applications folder, which isn't. Presto, the fonts are getting the "serious problems, do not use" error message.
Not quite, at least as I understand how an iCloud Drive works. The folder is local on your Mac, but when you place anything into that folder, it is copied/synced to iCloud. The question then is, why is the simple act of placing fonts into the sharing folder damaging them?