I seem to remember from a thread on the WiFi version that there was a writable data file on the Kobo that contained the info. about what store to use, and that this file was in fact updated every time that the Kobo Desktop application was used.
(Thread was
https://www.mobileread.com/forums/sho...d.php?t=113151)
The file in question was \.kobo\Kobo\Kobo eReader.conf
If you were up to trying an experiment, take a look at this file (if it exists), then try a sync with the Borders desktop application, and then look at the file again.