This is just a limiter for ground jump cancels, you can't do more than one, ground to air, jump cancel. For example if you were to transcribe the string to text, and you separate the two types of jump cancels to ground and aerial, gJC must not appear more than once.
Another string for Nanaya that demonstrates this is (CH)5c gJC->IAD j.b 2b5c5bb 22c 9 j.bc aJC j.bc airthrow.
Note that, even if you used 2a 5a 22c to do a free action jump, this does not reset the ability to re-ground jump cancel. Until "N Hits!" disappears, valid or invalid hits regardless, the limiter will still apply.
As for Shiki's 5bb(5a/2a) whiff, you'll notice its special that it is not counted as a reverse beat or is it penalized. Its just the exception, and part of 5bb properties.