With the announcements of the releases yesterday from both The Unwound Future (DS: Sep 20, 2010) and The Mask of Miracle (3DS). What is going to happen to The Specter's Flute? Will it end up in the DS released between the two or will find its way to the 3DS?

Time will tell. What do you think?

I don't think they would release 2 Layton games in 1 year, so if Mask of Miracles is released next year expect Specters Flute to follow the following year, or vice versa

You will need two (even three??) releases within in a year, though it all depends when they release the 3DS. This is what happens when you have that delay between the games and the Japanese releases. And the thing is that The Specter's Flute is a prequel to the series showing how Luke becomes the Professor's apprentice, setting the story for The Mask of the Miracle.

I though it could be interesting to think about the dates, because knowing this could help determine the release of the 3DS.

Actually, I could see Level-5 releasing both simultaneously later next year.  Being on different systems gives them a little leeway, and they could save money co-promoting both at once.