[cfillion]

I've reduced it to the following steps and minimal scripts:

1. Run Script A.lua:
   

   function loop() reaper.defer(loop) end
   loop()

2. Run Script B.lua (with the correct command ID for Script A.lua):
   

   reaper.defer(function()
     local cmd = reaper.NamedCommandLookup("command ID of script A here")
     reaper.Main_OnCommand(cmd, 0)
   end)

3. Select "Terminate instances"

Maybe you could message the main script to terminate itself using a temporary extstate instead of re-running it?