Michael,
Just to make sure you have all the details you need, Amazing Charts comes packaged with SQL Server Express Edition, which is free. The Business Intelligence tools of SQL Server are in Standard or higher Editions. Those are not free and do cost money. Furthermore, Amazing Charts does not publish the SA password for their instance of SQL Server - something I vehemently disagree with - so you will have to have an automated process that, after backing up,:
1. Shuts down the Amazing Charts SQL Server instance
2. Mounts their database in your SQL Server instance.
3. Unmounts the AC database from your SQL Server instance when you are done.
4. Starts up the AC SQL Server instance.
. . . So that way you can have a fully automated procedure that pulls data from your HL7 files into AC.
You are correct that you would have to learn a new platform. However, I can assure you that when it comes to moving data, SQL Server Integration Services is truly the way to go. Those pictures don't even begin to scratch the surface on what you can do.
JamesNT