I never used the Sony Reader software and the direction is from PC to Sony - only.
The PC recognizes the Sony as a mass storage (one drive per memory) and via explorer I drag'n'drop the books onto the Sony.
After disconnection, the internal FW of the Sony takes care of the books I added and creates all the records it needs (thumbnails, various info etc.).
I never used calibre for this either.
Never had any issue in many years of use, T1, T2 or T3.
Only when the books are to be replaced (updated versions) one may have some issues, in particular when other items have been added, like handwritten notes. I therefore delete the books I intend to replace via it's own method, then drag'n'drop the new ones.
If the books are encrypted, I decrypt them before.
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