There are more transformation tools than you can imagine for EMF, its kind of crazy...
For metamodel to metamodel transformation where the models are not very similar:
If the metamodels are very similar and you only need to tweak some things then there are tools targeted that type of migration/updating:
- ATL now has a refining mode
- Epsilon has Flock
- Edapt looks very interesting as well because it does the metamodel/model changes together. It lets you work on a tree view and comes with a set prebuilt set of rules.
- Henshin which lets you operate on a diagram view of the model
- EMF Refactor is a more code-level approach, that can also use Henshin rules somehow.
You can always directly manipulate the metamodel and model using the EMF Java APIs as well.
I'll add, if you are doing any real EMF work you will need to get and read EMF: Eclipse Modeling Framework. It's available in Safari also. I highly recommend Safari, for $39 a month you get almost every development ebook you could ever use.