In fact you can easily go to your %APPDATA% folder or Library folder (for MacOS) and find the .gitkraken folder. There there is a profile folder and then your profile guid folder. The directory should look something like this:
%APPDATA%\.gitkraken\profiles\<guid>
or
Users\<user>\.gitkraken\profiles\<guid>
Inside this folder you can find a localRepoCache file. Remove the entries that are duplicated, then go back to Gitkraken and add them back as needed.