In 4th Monster Manual, the Dragons all have an ability that recharges their breath weapon and has them use it interrupting flow of combat. Does this use expend any charge they may have built up before being bloodied? For example, if the Dragon had their breath weapon recharged, when it goes into bloodied, once it completes its bloodied breath, will it still have a breath weapon charged?
No, the breath weapon would not be charged.
The breath weapon can only be charged or uncharged.
Taking the Young Red Dragon as an example, first the regular charged action:
Breath Weapon (fire) Recharge 5
and the triggered action:
Bloodied Breath Encounter
Trigger: The dragon is first bloodied.
Effect (Free Action): Breath weapon recharges, and the dragon uses it.
Per the rules, the recharge roll is done every turn regardless of whether or not the power is spent (Rules Compendium p91):
At the start of each of the monster's or trap's turns, the DM rolls a d6.
There is no note to only roll during turns when the power is uncharged. This makes the situation very analogous to the triggered action which might also recharge a already charged power. Either way, if the power is used, it is spent. You cannot store up charges.