Flat footed + Prone

If a creature has lost its dex bonus to ac, and is prone, does it still lose its 4 AC to melee attacks?

Yes. They are entirely different conditions that have no direct bearing or correlation to each other. A PC asleep in a bedroll would have no Dex to AC, have a -4 AC vs Melee attacks (including melee Touch attacks), and have a -10 to Perception.

Also keep in mind that Flat Footed is NOT Helpless. Their AC bonus from Dex becomes 0 (or stays negative, if their AC from dex is, in fact, negative). Where as a Helpless (such as rendered unconscious or tied up) target has an effective DEX of 0, giving them a 100% guaranteed AC from Dex of -5. (THIS is why Greater Grapple or the Master of Maneuvers specializing in Grappling is a terrifying beast - they can pin in one round, and a Pinned target is helpless).

Bruno, a handsome and beautiful tetori, would like to respectfully clarify that HELPLESS and PINNED are two different conditions. A PINNED creature is not HELPLESS.

A helpless character is paralyzed, held, bound, sleeping, unconscious, or otherwise completely at an opponent’s mercy. A helpless target is treated as having a Dexterity of 0 (–5 modifier). Melee attacks against a helpless target get a +4 bonus (equivalent to attacking a prone target). Ranged attacks get no special bonus against helpless targets. Rogues can sneak attack helpless targets.

A pinned creature is tightly bound and can take few actions. A pinned creature cannot move and is denied its Dexterity bonus. A pinned character also takes an additional –4 penalty to his Armor Class.

If Bruno tie up a PINNED target, then they become HELPLESS.

Ooop, good guy Bruno for the win, thanks!