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Originally Posted by durtreg
1) change the title of say book X in calibre, then I quit calibre, go to its library Folder on the computer, find book X, right click and have a look at it's properties "title" in Windows explorer as well as my pdf Reader. The title stays empty.
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Read the above posts explaining when Calibre updates the metadata inside the files themselves. This is expected behaviour. Actually, you're not even supposed to care about the files inside the Calibre library, instead interface with it using either the GUI or the CLI tools.
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2) Do the same, but instead of quitting calibre I just send book X to the device again (it was already there)
Now I have two books on the device with different names (this might be the reason for my disappearing bookmarks/notes). The new one has indeed the changed pdf title (as opposed to the local file in the calibre library on the computer)
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If you changed the title, this is expected behaviour as well: Calibre computes the path according to the template you specified in the send to device- options. If the path is dependent on the title and you change the title, the old file will not get overwritten, instead a new one will additionally be written. That file, as you have seen, will have the updated metadata.
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However some questions remain:
1) why isn't the local library changed (the pdf property on the PC). The name of the pdf is changed. I would expect the properties also to change or at least have the option to write all properties into the files
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Because of the Calibre design philosophy. The library is seen as a database without user access.