Surprisingly this problem of treating EDI files as lists instead of the tree structure it actually is, is widespread even among clearinghouses. In retail energy, clearinghouses would often support their own custom format, which typically was either CSV or Excel. If you used that, you would routinely run into data integrity issues.

At this point, I'm pretty convinced that if you're running into EDI (or its sister formats like HL7) processing issues, its because you've got the wrong data structure in place or you aren't keeping your rules up to date. Once you've got the right architecture in place, you can easily manage 100s of provider/partner-specific rules with one person at 20% time. If you don't your whole company is going to be dealing with data integrity issues forever

Care to share what "right architecture" could look like? There's surprisingly little public engineering reading about EDI...