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hi thanks, you're of course very welcome here

and yes, the issue is exactly about two (or more) sound-cards having the very exact system name or label ("M Audio Audiophile 24/96"); qtractor search for this name and matches the first one it finds around at the time the session gets re-opened any time later on.

i'm afraid it is not possible to change the name of an ALSA device so you'll probably stuck with that shortcoming as is. sorry

but maybe, just may be one solution for this kind of conundrum: I would try to have at least two "Midi Through" ports as possibly given by the following entry in /etc/modprobe.conf

one for each of the MIDI ports of the existing identical soundcards and redirect and connect them permanently on system startup or using your favorite patchbay application ;), like this

1. connect first 14:Midi Through port 0 to first 16:M Audio Audiophile 24/96 MIDI port 0
   aconnect 14:0 16:0
2. connect second 14:Midi Through port 1 to second 20:M Audio Audiophile 24/96 MIDI port 0
   aconnect 14:1 20:0

from this moment on you could resort to use Midi Through port 0 and 1 to route the session's top and bottom synth buses respectively.
got it?
hth.
cheers