boxcorner: I have never done it myself but I know that (as itimpi mentioned) there should be an option to format the internal memory directly in the Sony reader. Since it is directly on the device, thus from Sony developers, I assume it should be safe to use. Nobody on this forum can provide any warranty though - you may want to contact Sony support if you want to be 100% sure.
You are saying that Calibre and the reader do not work well together but from what you mentioned so far it is actually not a problem between Calibre and reader but either a problem of the reader or between the reader and the OS. Does standard copying via USB (outside of Calibre) from your PC to your reader work? If not, then you can be sure that the problem is not in Calibre.
EDIT: I just found a closely related thread - you may find it useful:
https://www.mobileread.com/forums/sho...d.php?t=100767