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With the caveat that I'm not a developer and don't know the insides of the program and all my knowledge about it could be wrong...
It sounds like your database is not syncing. IIUC All the metadata and book info is stored in the metadata.db file which is an SQLite database. How have you set up the data on Dropbox? Did you also put the metadata.db file there to be shared? Also, do you completely close the calibre program when finished with it? Not just the gui and have the program run in the background, but close it completely. I'm not sure about calibre, but many programs that use data files keep them open in memory and only sync to disk periodically.
What may be happening is that each calibre instance holds the metadata.db file open and then at some point syncs back to disk, but it hasn't yet seen the updates from the other instance. That means they're writing old data and updates don't happen. To fix that you'd need to completely shut down one instance of calibre before opening the other.
I hope this helps.
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