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1) Calibre "sees" only books it knows are on the device, because on connection it runs a metafile-update and compares which of the books that should be there actually are.
2) Calibre creates an own file system on your reader which you can influence via "Settings-> Store books on device" (don't know the exact english name)
3) Tagging books via Calibre to show up in the Library only helps with epub files, all other formats are ignored. According to 2) you can set {tags}/{authors_sort}/{title}, the you have it at least in the files directory
For the Freebooks I suggest you import them into Calibre when the device is connected, then you delete the original installed ones language by language, each time you connect it to your PC. So the amounts are not to big and your devices is relative sure of freezing. If it happens nontheless, I made the experience it is quite helpful to have only some books in the "favourites" folder and connect it to the PC only when on the main page. If it freezes after disconnection just turn of, then on again. Normally it will boot up to the main page and only freeze again if you enter the library, but if you go via favourites it normally works. If you use an SD card it is helpful to restart it once inbetween without the card. And NEVER remove the card while it is switched on, even when it is apparently dead.
I hope I could help, troll
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