I can not rename the queries that i have configured in the Index. This is a bit annoying, as I have to set up a new query from scratch just to be able to give at new title.
Yes, we made it with files and the name is the name of the file. And the reference is directly to the filename. Maybe a bad design descision.
Anyways - you can locate the .query files in /Files/System/Repositories and rename it there. Remember to update any references you have to that search.