OK, so since I had a few headaches with my legacy SD cards from the earlier firmwares, I did some testing. I thought I had a bug with recalling the state of the sequencer but I think it’s more so in saving sequences. This seems to be repeatable for me:
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Format SD card, plug and unplug USB.
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Create sequence and save to the SD Card. In my case I left pattern 1 as 16 steps, played some piano chords on Track 1, changed Track 2 to mono and Octave to -2 and played in some bass notes, changed Track 6 to drum and step entered some drum notes
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Exit Pattern Edit mode
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Save sequence to SD Card as TEST
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Reload sequence from SD card. Track 1 and Track 6 patterns are now empty.