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You can, of course, connect any ALSA sequencer client/ports as you want. In fact, ALSA-seq connections predates JACK-MIDI by many years in QjackCtl implementation ;)

However, whether the connection does not persist or shows in the ALSA Connections tab window is odd.

Check your current Patchbay profile, maybe there's some rule re. Yamaha USB MIDI and/or ZynAddSubFX marked with the exclusive bit?

Cheers