Several different aspects to this, but here are some points to consider:
How hard is it to get the patient data out?
How much will it cost you per year to run your old EMR as an archive?
How much data can you get out to bring over?
Of the data that you can get out, how much of it can you match up and get into AC?
Conceptually it is significantly better/easier to run one EMR, but that may not be practical for you.
