[tomsem]

Amazon does not care at all about your side-loaded content when it comes to Cloud Collections. If you want it to track your personal content in collections, use Send To Kindle and store it in the cloud. Otherwise it is vulnerable to getting disassociated from the collection you try to put it in, since it is not something Amazon keeps track of. If you have calibre inserting ASINs to trick Amazon into syncing those side-loaded books between devices (even though it is not stored in the cloud), that may be another variable and I don't know what effect it would have on this one way or the other, since I don't use that calibre feature.

But first, a reality check: when you tap the Content filter/Views dropdown selector (with All Items, Books, Periodicals, Docs, Collections, Active Content) and select Collections, do you see your collections listed? if so, all is well, or as well as it can be given there may be issues with side-loaded content. Select one of those and you should see what is in them (greyed out if they are not on the device). If you want the collection to 'Show in all Views' then select that option from the menu. Show In All Views is a tricky feature that only occurs on Kindles, so it can be a little confusing or obscure if you are used to how it works on all other devices/apps. But assuming your collections are NOT showing there....

The next thing to check is that I thought that there was a firmware update for the current Kindles which made it possible to 'hide' any cloud collection from displaying on a particular Kindle. So there was a way to 'remove' it (from the device) as well as to 'delete' it (from the cloud). And there was a way to un-hide it (restore it from the cloud). However I do not have a current generation Kindle to check this on, and cannot find any actual reference to such a feature here or anywhere else, so it is entirely possible that this is a false memory or a true memory about some discussion of a hypothetical feature, albeit one which if it were to actually exist, could totally explain what you are seeing. Surely someone with a current Kindle will read this thread and can confirm if it is a real feature.

Did you ever de-register the 'problem' kindles? I would do that, then Reset. In theory, Reset de-registers as well, but it might be worth trying explicit de-register first. That will clear out pretty much everything for a fresh start. It will download and index the default dictionary for the language you choose when setting it up. Then you can add something to the device (from the cloud) and see what collections it is in.

I have never done a Reset myself until just now, but it is probably not a bad idea to do one once in awhile just to clean up garbage files. A few months after I got my Paperwhite 1, I ran out of space and discovered a bunch of zombie files that were chewing up several hundred megabytes. I deleted the files 'manually', but I'd probably use Reset next time. Of course this only works well if you have collections set up that can manage your reading workflow (To read, reading now, reading complete, reading suspended etc.)