The reason for the trap is to compensate for the negative pressure the drain line is under. Since the blower is pulling the air, if the trap wasn't there, then the drain wouldn't drain properly.
By having a trap, your blower is pulling air back through the trap while the condensate water is allowed to flow and drain.
With that being said, if you have water forming in your emergency pan, its an indication that the main drain line is clogged up. If you know where the drain line exits the home, take a small shop van and vacuum out the drain line. If its really backed up, it will sound like a golf ball through a garden hose.
If your trap has a clean-out installed, I would recommend pouring some hot water and bleach combination down the trap itself after you have cleared and flushed the drain. The bleach will assist in killing any mold/mildew that has accumulated in the drain.
Also, while your in your attic, ensure your emergency pan has a float switch and that its operating properly.
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