For traslating Allegro database, You may output .dsn file from Allegro and import it to Hyperlynx to avoid Algbrd2hyp translator's bug in intepreting arc traces(see my previous post). This flow works well for Allegro 14.X,15.X and up-to-date 16.2.
For creating a chain channel in the freeform schematics, You don't have to worry how different stackups of two boards be. U can Create a virtual stackups by adjusting individual layers thinkness to match the real pcb's stackup. However, You may find you can't add different vias in the freeforom schematics. To create different vias, you need to edit .hyp file manually.
BTW, I suggest you contact Mentor AE to get hands on. If You live in China, I suggest You call Dr. You who is very familiar with Allegro and HL.