I've been playing with this and managed to get it to work on a single domain.
I noticed most of the files had a hash at the end of them, so I merged them all down into a single .docarchive file.
Of course, this may break in the future, but for now it works
# Delete existing .doccarchive
rm -rf templates/AllProjects.doccarchive
# Create a working folder
mkdir templates/working_dir
# Copy most files, excluding the index and metadata.json files to the working directory
rsync -a --exclude 'index.html' --exclude 'metadata.json' templates/ProjectA.doccarchive/* templates/working_dir
rsync -a --exclude 'index.html' --exclude 'metadata.json' templates/ProjectB.doccarchive/* templates/working_dir
# Copy across the index.html file from each Archive, but give it a new name when copying
rsync templates/ProjectA.doccarchive/index.html templates/test/projectA.html
rsync templates/ProjectB.doccarchive/index.html templates/test/projectB.html
# Create a new .doccarchive folder
mv templates/working_dir templates/AllProjects.doccarchive
You can then host this on your server and point to /documentation/ProjectA or /documentation/ProjectB.
There is one current drawback I can see, the table of contents isn't unique.