Initialize owncloud server for sync with data already on both sides

Hi all,
I'd like some guidance please... Have some experience with OC already. Now installing a second OC server on my web server that is meant to keep a data directory on the server and a data directory on my Mac synchronized. Both data directories already exists and are filled (with about 1.200.000 files / 30GB). I'd like to initialize the server so that on first sync the client recognizes all files as identical and won't upload or download anything (it would take ages for my line to upload 30 GB!).

I think (but don't remember exactly) that I tried is already with my first oc server by:
- Copying the data directory with all these files into the main data directory (on server)
- Copying the data directory with all these files into the main data directory (on Mac client)
- Server: occ files:scan
.... which took ages and – IIRC – never finished
and while this was sitll working, or maybe I shut that process down, I let the Mac OS owncloud client check for differences and that also worked forever, so I finally shut down everything, reinstalled owncloud from scratch and removed that large directory again from the repository.

So now, for not affecting my main owncloud installation, I want to try anew with a second server instance.

How should I proceed?
The second instance is installed already (using MySQL). Both directories are ready.
What are the next steps to do it right?

Thank you very much!

This feature was often requested. Recently checksums have been integrated into ownCloud, so it should be possible, it just needs someone to implement it: