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@Dopedangel : If the junction trick doesn't work out (I was going to suggest a symlink, but dropbox may follow them), try a using a file sync tool that a) gives user control over what gets synced and what doesn't, and b) interoperates with cloud service providers.
Goodsync can do it, I use it to selectively sync to my FTP service provider. Not free, but nor is my FTP service provider - 25+ years of trouble free service earns loyalty.
Also I would have thought this thread belongs in the calibre forum, rather than here, given its primarily about calibre portable.
BR
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