Talk to your vendor about their experience and don't be afraid to ask around. Vendors like to exaggerate their numbers, so view 3rd party numbers such as the Vendor Market Share. Vendors with less than 750 physicians can be considered "unstable" as there have been many cases in the past of vendors smaller than this size going out of business.
Do you know your rights if you ever want to take back data from your vendor?
The truth is, you do not have many options if your vendor does not want to cooperate.
Select an EMR that has an open ability to download your entire system data. Request from your EMR vendor to provide any encryption keys required to access the database. Ensure this is built into your contract and you have the vendor impliment upon going live.
Data migration is not something all vendors have the skill and experience for. As for references specifically for data migration as there are many vendors who cut corners offering migrations for pennies on the dollar. If someone is quoting hundreds of dollars for the migration of a full EMR be careful of their experience as data loss could be a real possiblity causing an impact in your ability to practice.