For many years I've been using Thunderbird Saved Messages with many subfolders. There seem to be several major problems. (1.) The only apparent way to move a message from one folder to another (e.g, from an Inbox) is to drag and drop. However, this is very tricky with the messages often being dropped into the wrong subfolder or, occasionally, to the great bit-bucket in the sky. (2.) When moving something into a subfolder, sometimes instead an existing subfolder will mysteriously become a sub-subfolder of another subfolder. The only way I've found to get it back to normal is to drag it up to the main Saved Messages line. However, when its near the bottom of my rather long subfolder list, I have to drag it in stages to get it to the top. This whole thing seems to have become more troublesome with the new version of Thunderbird, and yes, I'm using the latest update.
My suggestion is to allow standard copy and paste to move something from one folder to another (e.g., CTRL-C or CTRL-X and then CTRL-V using the clipboard if necessary) at least for saved messages. Drag and drop is messy in most cases, and this would allow it to be bypassed.