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If you did a complete reboot, there are very few ways that the server would not see all the books you see in the GUI, so start there - Can you see the books in the GUI? If yes, then I suspect one of these:
1) you are running a different library on the server and the GUI, or
2) you have a restriction set for the server.
If not, then you need to track down why they aren't in the library.
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