Definition of "Phantom Folder": The term "Thunderbird Phantom Folder" seems to be a standard expression (and you will find hundreds of hits in google -- it's extremely strange that there is no StackOverflow entry for this yet). It refers to folders that appear in gray and italics font, and apart from possible subfolders, they do not contain mails. Phantom folders can not be deleted. Most importantly: they do not exist! This is why they are called "phantoms" because Thunderbird shows them although they are not for real.
Some technical notes: I'm using Thunderbird 68.2.1 (64-Bit) under Ubuntu Linux. My IMAP mail account is run by "outlook" if that makes sense? (I'm not an admin...) I also have an outlook email client on another Windows computer, but it is being turned off while I'm experiencing or trying to fix these problems to prevent any side effects. None of the described issues appears "online" (in the outlook web mailer) or in the outlook mail client, it all just appears in Thunderbird.
Standard Problem: Well, the problem is simply the "existence" of the phantom folders, i.e., that they are shown although they do not exist on the server. (I assume an IMAP server.) That is, the question everyone has is how to make Thunderbird understand that they are not real and thus to make it remove them.
Solution: The internet is actually full of dozens or hundreds of posts, which essentially all tell the same (I think I've almost read them all^^). So please, just google "Thunderbird Phantom Folder". Anyway, here a short repetition of what you are supposed to do, but please don't expect details, just google it.
From all that I've read this seems to work for pretty much everyone. But...
My (Non-Standard?) Problem:
[1] In a very nutshell, my problem is that all the countless google hits on my problem simply don't work on my system. Most importantly: All these solutions seem to suggest that it's a local problem with my local Thunderbird installation. After days of (unsuccessfully) following instructions, I started questioning that premise. So I've installed Thunderbird on a fresh PC and added my mail account. And it downloaded the phantom folders! So this proves it's not a local problem! Thunderbird must have uploaded the (flawed) folder list somewhere, which is probably the reason why deleting all the local Thunderbird files did not work as expected. Subsequent research suggested that my issue is related to the list of subscribed folders (later more).
[2] Furthermore, and this is extremely(!) annoying to me, whenever I rename a folder, Thunderbird creates a phantom.^^ So if I create "testfolder-1" and rename it into "testfolder-2", then I have both, where "folder-1" is a phantom that I can't delete. That behavior is also true for the phantoms themselves. So let's say I rename the phantom into "testfolder-1new", then I get a new phantom with that name whereas the old phantom "testfolder-1" remains as a phantom.
Details/hints for solving the problem: As said, I believe that the problem might have to do with the list of subscribed folders. However, that doesn't really help me because in the subscription menu you only can check or uncheck the folder names, but I do not just want to not see them, I want the issue to be resolved. That is: what should be possible is that I can eliminate those wrong lines with the phantom folders and not just checking/unchecking the respective entries (but this is not possible anyway because the phantom lines do not have a checkbox next to them). An option like "re-compute the subscribed folder list" would solve the issue I suppose, but this does not exist. And, as said, deleting all the local files and then rebooting thunderbird does not help, so maybe it will just download the flawed subscription file(s) again. I would also like to note that there is an option in the account setting stating "show only subscribed folders". If you uncheck this, all folders on the server are shown. Non-surprisingly, the phantoms disappear (this is actually the reason why I believe the issue is caused by the subscription list). However, obviously I do not want to see all dozens of useless IMAP folders, I really do want to see only the subscribed folders. But if I switch back, i.e. enabling that option again, then sadly the phantoms re-appear.
So, it all boils down to two questions, both of equal importance:
How can I finally get rid of these phantom folders? More specifically: Is there a way to force Thunderbird to re-retrieve the folder list from the IMAP server?
How can I prevent Thunderbird from creating a phantom every f.... time I rename a folder? (And just because I am very interested: What is causing that error in the first place? Is it an actual Thunderbird bug?)
I'd deeply appreciate the help, this is seriously driving me crazy.
Worked for me: