Getting the data over takes some API.
I think the "human interface" is always the biggest challenge. i.e. you called it "Matl", they called it "Material", etc., You use A.1, A.2 as a revision schema, they used 1, 2, 3....then trying to get common titleblocks....
So it gets easier if you still keep the data rather separate. Your data is in a directory off of the root, and the new company's data is in a sibling folder off of the root. That way you can have your datacards and workflows and they can have theirs.
If you want to combine everything you'll need to be able to map datacard field to datacard field, file property to file property, workflow state to workflow state, revision schema to revision schema, etc.... Almost as hard as the data migration itself.