In order for us to provide better support, we need to see the log generated by Citra. This guide will walk you through how you can obtain the log file: How to Upload the Log File.
You can only change it when the game is closed. That is why you have this hint here:
Also you should not open the same citra-qt, extract a standalone build by going to the download page then click on “manual download”. After you have extracted, create a new folder called user where that build’s citra-qt is at.
If you want to copy the saves, open the main Citra (the one you had before) then File -> Open Citra Folder then copy sdmc folder into the newly created user folder.
Now you have two Citra builds with their own user folders so console IDs won’t be conflicted.