One thing to consider is it will change the way keywords have to be accessed in Unity Script (or external programs using the OnBase API). It would require analyzing any code that accesses or modifies the keywords on that document type.
Also, if you have any SQL statements written that do any retrieval from the current keyword tables those will need to be re-written.
As far as changing the documents, it will probably change the way the keyword panel appears for that document type, as the keyword group keywords will now display together.
Behind the scenes what migration does is move the keywords for a document from their own database tables to a single table (for the keywords in the keyword group, any other keywords not in the keyword group stay in their own tables).
Hope that helps a bit.
