You only need to delete an existing GCD from .System if you (i) load by gupdate.gcd in Garmin folder on SD card, or (ii) by RGN via Updater.exe in preboot. If you load either by dragging the GCD onto WebUpdater.exe (or it's desktop icon) or by pasting it as 'gupdate.gcd' directly into .System then the existing gupdate.gcd is overwritten. If you use the other mentioned methods without ensuring removal of it then it'll likely simply flash back to older version which is what's happened for you.