I know that it is too late to answer this question, but perhaps my answer will help others.
I recently ran into the same problem. Then it became regular. I did not find a solution to the problem itself, and this can be caused by many different reasons, therefore, probably, a universal solution does not exist.
However, there is a way to save your files while notepad ++ is not closed. Even if the backup folder is empty.
First of all, do not close Notepad ++. Open the task manager, find the notepad ++ process and find the Dump or Create dump file option. Click on it. This will result in an entire process memory dump. This dump will contain the documents that you have opened. However, you may need to find this data, and may also be in a different encoding. I think this is in UTF8 most of the time, but I'm not quite sure.
The dump file can be checked using simple programs such as notepad ++ itself or a hex editor.
Aneri Jan 16 '15 at 21:00 2015-01-16 21:00
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