I understand what the error means, and I've run into it legitimately before; however, I don't believe this time is legitimate. There are no references to any NS module outside of any of my entry points. Worked fine before; added a new function to the module and started seeing this error.

I can say I've seen this a lot. Also notable whatever validation NS puts script code through is different for uploads to the file cabinet than it is for editing a script from the script page. I've seen the same script error with one approach and not the other. Also note I've seen netsuite improve (i.e. reduce false positives) with this. I had a case where some code I had compiled to UMD was confusing netsuite and causing this error even though the code was known to be working. They eventually fixed it so now no such UMD code breaks. I think their validator must be very primitive.