Apologies for missing this message! If you search for HL7 (the magnifying glass in the upper right menu), you will see several posts here. In addition a search for 'FileMaker HL7' will give you some more possibilities. For example there may be systems that don't use FileMaker directly, but can integrate with it (through ODBC, or JSON or XML, for example).
I have integrated HL7 with a client's home-grown solution. As they are a lab that deals with physical specimens sent in from their clients, they do not need to decode any HL7 Requests. That means we have much more control over the HL7 that we do do, because we create it.
So far I have integrated their solution with two different EMRs (across three clients) and the differences between them have been minor, so the approach I set up for the first worked almost perfectly with the second.
That approach is to loop through the segments as needed and build the elements. As each segment is built a script is run that creates a record with that segment's data including Base64 PDFs. When it it all done the related records are listed and concatenated into a text file that is transmitted via FTP to the client's system.
I did build a receiver for the system that we have never used, but it involved a library for how to read each element in each segment. The idea was to check the segment code and then run a script that would parse the required data points out of the segment according to the library of instructions. I never got a chance to test that, but it seems like a flexible way to do it, albeit potentially high maintenance.
That said, others on this list may have better ideas for you.