I moved a sub-folder (which also contains sub-folders) and now the sub-sub-folders appear empty.
This is a Thunderbird issue. I am running version 31.12, Mac OSX 10.11.3. I moved a sub-folder to a position under the name of the account in the folder pane. I can see the messages in the sub-folder but I can't see the messages in the sub-folders of the folder I moved. If I do a search on the sub-sub-folders, the search reveals the messages but I can't access them directly through their respective folders.
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There are several suggestions here: http://kb.mozillazine.org/Disappearing_mail The linked page about 'empty folders' may be especially relevant?