Problem with DTPO after moving groups between databases

I am reorganizing my databases. I opened all the databases, selected a group, and moved the group to another open database (prior to this I verified each database to ensure no errors). Following this, I was left with a number of documents left in numbered groups (e.g. 000001, etc) with similar subgroups. How should I have moved files? Each file individually, using the finder, etc?

Thanks.