Thank you all for the great responses, I did get it to work, I wish it were a bit cleaner but it does what I need it to.
I had to modify each BAT for all of the American Laser Games (9 I think total). So now each game calls to an AHK I was able to get working. The AHK runs my key reprogram then I used winwait to keep an eye on any window that starts with “DAPHNE”. When daphne closes, AHK senses and triggers the reprogram back.
The BAT continues to load the game as AHK waits in the wings, listening to the daphne window.
So not a huge deal as there were only 9 games but if I wanted to do something similar for an emu system wide, well… it would certainly be easier with pre/post emu commands within HS but if they are there, I can’t find them.