This is how I do (I also replied in that forum):
1. first delete the books to be deleted/updated/replaced on the Sony (I meant using the Sony itself).
This way the Sony cleans itself the data, all data, all notes, all everything.
2. Then connect it to the PC.
As I do not use calibre I close it first.
3. Upload the books onto the Sony (it needs first to accept the incoming "friendship request" from the computer
)
4. Use the correct USB eject method, to make sure all handles are closed and all allocation tables were fully written.
5. Then the Sony works by itself in its own way (it will take a while, depending on the number of book added - I add some 2-5 at once so not big loss).
Never had any issue using this method since I started using it, years ago. Never used calibre nor Sony companion software to do things on my T1/T2/T3 devices.