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Not really sure about the nature of the problem.

I ssh to a remote machine. Issue a

cd ~/Dropbox
cp -r ~/Documents .

and getting messages of

No such file or directory

for specific files during the copy.

Also I seem to be getting different file sizes for the two folders,

du -s ~/Documents/
7894448 /Users/cue/Documents/

with the one in dropbox being larger

du -s ~/Dropbox/Documents
7974480 /Users/cue/Dropbox/Documents

The source folder is on MacOSX if that makes any difference.

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Could it be files with names that don't agree with Dropbox or that aren't handled properly by the unix shell cp command?

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Mac OS still uses resource forks in some cases. OS X comes with a copying tool called ditto that helps with copying those files.

ditto will preserve resource forks and HFS meta-data information when copying unless instructed otherwise using --norsrc.

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