After the 7/17 patch, my launcher is in a repair tool loop whenever I try to update WoW.
I uninstalled launcher and tried again and it continues to restart the repair tool.
Occurs even after I uninstalled Classic.
My guess is because you manually deleted the wow folder from the incompatible issue you noted, though this probably should have been posted in tech support also.
Try restarting your computer, use the windows option to uninstall the bnet app, then reinstall it, and see where it goes from there.
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It was in the repair loop before I deleted any folders.