There are not currently any scripting capabilities in HyperLynx. Eventually, HyperLynx will support this type of functionality, but not immediately. If you can tell me what you're trying to do, I may be able to help you with some other options.
For instance, you could create 100+ transmission line paths in a single FFS file and simulate once. Or you can export that FFS schematic to a .hyp file and run each net individually in the batch simulator in BoardSim. Another option is using the sweeps engine in LineSim, but if you need to actually switch the IBIS model that is used, that probably won't work for what you want to do.
I was not able to open more than 3 instance of hyper lynx .how to open multiple instance of hyper lynx line sim as well as board sim