Well, your answer is better than the one I was about to offer. I called TD Ameritrade for this exact reason more than once and was told that in the penny stocks the market makers can do whatever they want (which frustrated me to no end). Basically, live with it or stop trading pennies.
This happens to me all the time - my initial order is of sufficient size to show on L2, but then I get a small partial fill and the remainder no longer qualifies to show on L2.
Some of these are presumably legit partial fills, but I beleive that some of them are due to an MM giving me a partial fill so that their bid/ask shows on L2 instead of mine.
I don't think it relates to "priority of execution", but rather to whether the (remaining) order even gets "marketed" to other MMs via L2.
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