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...the snapshot feature you opt when creating a new patchbay definition profile is not quite an accurate connections saver as you might expect.

Aha, the world is round and ever changing: as of QjackCtl 0.3.3.14+, CVS commit-log:

- At last, after years of retarded procrastination, the old infamous patchbay snapshot feature has been the subject of a almost complete rewrite and it does try to give a way better mapping of all actual and current running client/port connections, both JACK (audio, MIDI) and ALSA MIDI, of course ;)

Cheers!