Are you sure these are the settings before you deleted it? There wasn't much in there but maybe you hadn't used it much. Local storage settings don't seem to be the culprit in this case.
If you backed up the whole appData directory I'd love to see the whole thing. I'd like to get to the bottom of this.
I think qrc__0.localstorage is the only interesting one. Attached you find a new zip file with the qrc__0.localstorage from my backup. I'am not 100% sure, that the first zip file is the right one. I hope it helps.
Sorry to dredge up an old thread but this just happened to me and I fixed it by deleting everything in C:\Users\mpflaging\AppData\Local\Sencha\Sencha Architect 3.1
But I did back it up. See attached. I had to take out the file "xds-3.1.0.001851.ion" (57Mb) and the subdirs (23Mb) because your site does not allow files above 488.3 KB (and also fails silently if this is exceeded).