First: some questions:
- Are all the books epub? I suspect that the ones with the missing covers are probably mobi, although the fact that the local library cloud connection identifies the books as already in the library argues against that.
- Do you have any plugboards defined?
Now to the main issue: as far as I can tell this situation can happen only if calibre is not matching the books in CC's database to books in its library. To check this:
- Connect as a wireless device
- Let the connection stabilize
- In calibre, click on the device view icon
- Sort by "In Library"
- Check if all the books have the green check mark
My guess is that the books without covers will not have this check. If this is the case then the FAQ answer I referenced in post 4 tells you how to fix it.
If the books are marked as "In Library" then (probably) somehow CC's database was changed and CC's "last modified" date set to whatever is in calibre. In this case calibre and CC will believe that everything is OK. One way to force the last modified date in calibre to change is to create a custom column of any type, restart calibre (as it says), delete the custom column, restart calibre, then connect as a wireless device.
If you know which books in your library are supposed to be on your device then probably the fastest way to fix the problem is to resend the books. Connect as a wireless device, then in the calibre library view select the books that are supposed to be on your device and send them.