Think you should knock up schematic which will help you and us understand better exactly what you have in mind.
Like MC says if you don't clear the fault the PMDX will never come out of fault so you'll be stuck in a loop. This means you'll need to Kill power to the drives or use the Enable/reset option on the drives.but this may not suit your plans or the PMDX but without seeing schematic it's not so easy to see what your intending regards E-stop etc.