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I would suggest the following trick. Write a small batch file/script to launch calibre. Have the batch file check for the existence of a dummy file in the dropbox folder if it exists it should abort, if it doesn't it should create it and launch calibre. Once calibre quits it should delete the file.
Note that this isn't fully robust since the file isn't a proper lock file, but it might be "good enough" if only a small number of people are doing this.
Backup your calibre library often.
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