@Clint Hmmm...This could definitely be a problem.
As a general rule, when you are playing legato, you want the note-on message for a new note to happen before the note-off message for the old note. For example, that is how a monosynth knows that it should not retrigger the envelopes when the pitch changes.
But if the old and new notes are the same, I think that the way MIDI is designed is that the note-on message has no effect (because the note is already on) and then the note-off message turns the note off.
That suggests to me that changing fingerings to yield the same note should either send note off, then note on, or should suppress both of them. If the Sylphyo does not already do that, then I think that behavior should be treated as a bug.
I suppose you could use something like a MIDI Solutions Event Processor to massage the MIDI stream. It would have to introduce some latency, but remember that 1ms of latency has about the same effect as moving one foot further away from the loudspeaker.