It is probably sitting on top of the heat exchanger. I've had my heater box apart. There is not anything yo have to worry about with what you have done. the motor is off to the passenger side and will not give you a problem. You may here the flap move around with the blower motor on but it can't hurt anything.
But how did yo get the metal flap out? I had the box out of the car and removing the cneter vent flap required removing to the side pivot points, pulling the actuator arm off and then removing the flap. Was this done with the unit in the car?


To summarize no you don't hav a problem. Its sitting on the heat exchanger and can't get to anything

Dave

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1970 220D, owned 1980-1990
1980 240D, owned 1990-1992
1982 300TD, owned 1992-1993
1986 300SDL, owned 1993-2004
1999 E300, owned 1999-2003
1982 300TD, 213,880mi, owned since Nov 18, 1991- Aug 4, 2010 SOLD
1988 560SL, 100,000mi, owned since 1995
1965 Mustang Fastback Mileage Unknown(My sons)
1983 240D, 176,000mi (My daughers) owned since 2004
2007 Honda Accord EX-L I4 auto, the new daily driver
1985 300D 264,000mi Son's new daily driver.(sold)
2008 Hyundai Tiberon. Daughters new car