THis is a really nice piece of info on the backup functionality. I learned some things.

if your notepad++ backup settings look more or less like on this screenshot:

maybe a little explanation on how it works with these settings will help:
notepad++ makes a backup of all files that are not saved, every 7 seconds to %AppData%\Notepad++\backup like seen in this screenshot:

as soon as you save the file, the temporary auto backup will be removed from there (removed from %AppData%\Notepad++\backup, as it was saved already to it’s original location), and the previous version of this file will be saved to where the original file is located, but with an additional file extension .bak (eg. the previous version of myfile.txt will then be called myfile.txt.bak)

note: if your computer crashed before you could save any data, your unsaved files will be here: %AppData%\Notepad++\backup

if you chose verbose backup, there will be a new folder at your file’s location called nppBackup.
you will find all previous versions of your files there, meaning every time you save a file, the respective previous version will be saved there, with an additional time stamp appended to your file name. this type of backup helps if you have to revert to an older state and want to be able to open any past saved state until you find the “last working” version of it. (but this versioning consumes a lot of storage through time)

screenshot of a nppBackup folder with verbose backup (versioning) enabled:

What are your backup settings? What was your response to the prompt? What was your expected behavior? What actually happened?