Can you elaborate a bit more about the issue?
Have you used the Sync feature in the Desktop Modeler to synchronize the changes from both modelers already? Changes from both modelers have to be synchronized first before they are available in the other modeler.
And if so, do you get any error while synchronizing?
Wow, that screwed up things big time. I committed the desktop version, then synced so the web modeler would have the same project version after syncing, but it happened the other way round, the desktop project version got corrupted by uncommitted stuff from the web modeler.