Sometimes trading partners send incorrect EDI documents that fail syntax checking.  If you need to turn off syntax checking, then it needs to be done at the document level.  Log into your customer's account and navigate to "Document Types" in the left menu.

Once in Document Types, find the document you need to turn off syntax checking.  Click on the 3 dots to the right and select "Config"

Click on the "Document Type Configurations" tab.  Once on that tab, check the box called "Skip Edi Validation" and then save.