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hi, yes this is probably more on the Carla side of things and the way it doesn't not save/restore ALSA MIDI connections ...

maybe you can workaround that with:
1. QjackCtl Patchbay;
2. custom script using alsa-utils aconnect utility explicitly;
3. you could have it as a NSM session; but unfortunately there is no ALSA MIDI patch utility like jackpatch for you to preserve those kind of connections, so chalk this one off :)

hth.
cheers