The Differantial Setup make Hyperynx know which two nets be the differantial pair. For example, it will automatically select the differantial pair while doing net selection. Literallym it should correctly export the differantial pair to linesim after differal pair setting be done. However, It does't behavior correctly, you still have to explicitely assign the models to ICs to get work done. Another negative effect is that net statistics will report etch length as the sum of postive and negative nets, it makes you can't check statics phase of the differantial pair.
To generate EBD file, it's better to assign correct pin model.