[I have to change number formats because the forum likes to renumber things otherwise!]
Thank you for those very detailed answers! What I think happened here was … nothing in particular 
– just a bit of dropped bytes, and wear and tear, and data conflict and crankiness. It won’t be hard to get everything cooking again, but it will take a little time and effort.
(3) That’s probably good and correcting something that wasn’t properly aligned in the database. But all of that will be overwritten when we’re done anyway.
(3) On Anki Desktop – it sounds like what you ran there was a Check Media – a good thing to do (and it revealed another issue, see below), but make sure you run a Check Database too.
(8) That is a normal aspect of the automatic backup system. Since Anki is making local backups for you many, many times each day, it only backs up the database – your notes/cards/decks/settings, etc. – not the collection.media folder. A compressed database backup is probably under 20 MB, while the media for a collection could be multiple GBs. But this is only talking about the local backups – unless you turn media syncing off, your media will be included in a sync to AnkiWeb.
It sounds like there are a couple things to do to smooth the way to getting things in sync.
(9) On Anki Desktop – let’s empty out that old media! Because Anki doesn’t keep a backup copy of your media, it’s very careful about deleting any of your media, even if it seems like you aren’t using it. As a result, you have 18K extra media files in your collection! This includes things you’ve attached and later decided you didn’t need, but also every media file of every deck you’ve ever imported to give it a spin, and later deleted. But here’s the thing – all of those 18K media files have been syncing to AnkiWeb for the past 1.5 years, and now they are trying to sync to your other devices!
- In that Check Media window, there’s a “Delete Unused” button. Click that. [Don’t hesitate over this, because they only go as far as a “Trash” folder that doesn’t sync. If you find you did actually need them, we can get them right back!]
- Now run a Check Database, we want to make sure everything is perfect.
- Now force a one-way sync from Anki Desktop to AnkiWeb. We want your perfect database from here to be the one that AnkiWeb has.
- Keep an eye on your media size at the bottom of the page on AnkiWeb – that should drop significantly. Your target is the size of your collection.media folder in your profile on your Mac. Don’t be afraid to sync a few more times if the number seems like it can still go down.
(10) On your AnkiMobile installs, let’s clean them out completely. I know you already uninstalled, but the fresher they are the better, so you might do that again (uninstall, restart your phone, reinstall fresh). Or at least delete all of the notes and decks there and run Check Database again. You should also run Check Media there, and delete everything you find.
- By now hopefully it seems like things have settled down between Desktop and Web. If it seems like they are still trading files, keep syncing there until they are done.
- Choose just 1 of your iOS devices, setup syncing, and download-from-AnkiWeb. You should keep running sync again until Check Media on this device matches Check Media on your Mac.
- Then you can do the same with your other iOS device.
(11) After this, please be strict about syncing – especially because you will have 3 devices going at the same time. You should only have “changes” (edits, additions, review history, etc.) happening on one device at a time. None of them can sync with each other directly, so you need to sync with AnkiWeb when you open the app AND when you close/leave the app, on every device, every time. That’s the only way to be sure you are always working with the freshest version of your database, and you don’t end up with data in conflict or overlapping.