If I have multiple subfolders (multiple imports), and want to merge them into one subfolder so that all of the articles are in one folder instead of a bunch, how do I do that successfully?
You can just Select All and drag all items to another collection to combine them.
If you have a whole hierarchy that you want to combine, the easiest way is probably to temporarily enable the recursiveCollections hidden pref, make a temporary collection outside of that hierarchy, click the top collection (which should show all items within, thanks to the pref), and then drag all the items to the temporary collection.
And if you want to _move_ the references and not "copy" (though it doesn't actually create a separate copy, just adds the same reference to a different collection), you can press Shift while dragging.
Upgrade Storage
If you have a whole hierarchy that you want to combine, the easiest way is probably to temporarily enable the recursiveCollections hidden pref, make a temporary collection outside of that hierarchy, click the top collection (which should show all items within, thanks to the pref), and then drag all the items to the temporary collection.