It isn't open anywhere and making a copy in a different directory and setting is as the custom keys path doesn't work.
It gives the message on launch. Deleting from the Resourses folder and leaving the custom path still prompts it, as well as deleting it and not specifying a custom path.
The very first time I lauched the application I named the "keys" file to "keys.txt" and I got no such message on launch, but when I tried to recompile a Retroarch nsp it gave me some other error, which I can't reproduce now, because I can't even get that far
. I tried again and again a few more times and on one of the launches it showed me that message. I thought that I should rename "keys.txt"to "keys.dat" in hope of resolving the issue, but it didn't. So here I am now.