Create a file that contains the folders you want to withhold from the new repository
hg convert --filemap skipfiles "source folder" "dest folder"
Where skipfiles contains a directory of folders or files to not include in mercurial. This will create a new repository out of the old one and have no trace of those original folders in the new repository. Useful for making your repository smaller, if it gets too big.
Also, when using non code assets like images and other binary files. Try using BiTorrentSync This seems to be quite fast.