http://kb.mozillazine.org/Show_hidden_files_and_folders 

   Help > Troubleshooting information
   click on 'Show folder' 

   Close Thunderbird now.
   click on 'Mail' folder
   click on 'Local Folders' 

   Right click on file and select 'Properties'
   under 'Attrbutes', check it not checked as a 'read only'
   click on Ok. 

   right click on those files and click on 'Delete'. 

   Close the window. - top right X
   Open thunderbird. <<<<

I'm running up-to-date Sierra on a 2015 Mac Air. I'm bringing this backup computer up to date after my main laptop's untimely death. In Tbird, I created a subfolder; couldn't see it; so created it again. Then I could see both of them. I've tried to delete both, and - of course! - only succeeded in deleting the one that I wanted. Trying to delete it, I followed these directions, found in another support conversation here https://support.mozilla.org/en-US/questions/1090554: >>>>You can right click on folder and select 'Delete'. If this is not working try the following. Profile folders are hidden files and folders, so make them visible: http://kb.mozillazine.org/Show_hidden_files_and_folders In Thunderbird: Help > Troubleshooting information click on 'Show folder' a new window opens showing your Profile folder. Close Thunderbird now. click on 'Mail' folder click on 'Local Folders' Look for the file with no extension and also the file with same name with .msf extension that has the same name as the folder you want to delete. Right click on file and select 'Properties' under 'Attrbutes', check it not checked as a 'read only' click on Ok. right click on those files and click on 'Delete'. Close the window. - top right X Open thunderbird. <<<< I've done it several times. When I reopen Tbird, three "Nextdoor.mozmsgs" files have regenerated themselves. All this after trying the more intuitive step of right-clicking the folder and choosing "Delete". An error message briefly pops in from the right, that "the current command did not succeed", then something about the mail server. (I've never figured out how to grab and see an entire error message before it pops away again. This one ended in "...", so clearly there's more information to be had. Advice on trapping and expanding error messages is welcome!) So, two methods to delete a subfolder, and neither will succeed. The one I successfully deleted was where I wanted it - under Local Folders. The clinging one is under Sent Mail, under one of my three accounts. I'd love to know how to blow it out of there. Thanks!