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A safer alternative might be to run Calibre portable from a secondary folder, and use your choice of tools to run a manual sync to the Dropbox folder at the beginning and ending of your Calibre session. Depending on what software you use, it may be possible to automate this to some extent.
That way the changes propagate between computers, but you aren't running it inside Dropbox and risking the real-time sync fudging with things.
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