you can ignore files with the following command: 

git update-index --assume-unchanged path/to/instance.cfg

^ git ignore can only ignore files that are not on the repo at all, it will not respect files that are on the repo and always track changes on them. 
As a workaround you can instead use this local command that will make your local repo ignore all changes to a given file. 

To get the relative path of a file for the command, don't bother writing it out by hand, just right click on the file in the github desktop application in there will be a relative file path option to copy from. 
