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Originally Posted by kj_va
I think I previously should have mentioned exactly how I used Amazon Cloud: I use NetDrive2 to map my Amazon Could storage as a E:\ drive on my PC, so yesterday I simply moved the library from the local folder to a newly created folder I created on Amazon.
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Ahh, that means that almost everything I said isn't right.

I assumed that you were doing the "normal" thing: that you had a local copy that is synced to the cloud.
First note: calibre specifically does not support network drives. See the
calibre FAQ entry here.
Second note: CC depends on the cloud drive provider reporting a different "reference date" for a file so CC can know it changed. In your case I don't know what Amazon will report, or even if Amazon knows that the file changed. If it gives the creation date then CC will never notice the change. Resetting CC's cloud library should force a download but you said you tried that and it didn't happen, so it is possible that Amazon is not serving the modified file over the cloud access interface.
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I just now enamed my "Kindle Library" folder on Amazon to "Kindle Library2" and then upon starting Calibre received a "Corrupted database" error message and it would not open (naively thinking that renaming the amazon folder back to the original name would permit Calibre to open normally, but instead the program is undertaking what looks to be a multiple-hour database restoration).
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If the metadata.db file went away or was damaged on E:, calibre will indeed offer to rebuild it. It does this by scanning the entire library for "metadata.opf" files that contain the calibre metadata for the books, rebuilding the db from what it finds.
Why the metadata.db file was lost or damaged by the rename is an interesting question.
Things might go a lot faster if you copy the library to a local drive before you run the restore, but given that it has already started ...
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In any event, I think I will probably move the library back to my pc and set it up as a content server for remote connection.
Thanks again for your help/time.
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What you might consider doing is your own sync. You would indeed keep your library on a local drive. In addition, you would keep the E: access and manually sync your library to that copy. The sync would be done with some file sync program so calibre doesn't see the network drive. The page
What’s the best free file synchronization software for Windows? lists several good, free programs. I have used freefilesync, but be aware that it tries to install crapware. I just installed the newest version and it asked me to install something called "registry reviver", but gave me the option to opt out.
It is possible that syncing the library to E: will result in the same problem, that metadata.db doesn't appear to change. You can easily work around that by using a script that deletes the file from E: then does the sync.