THAT BRIEF flap late last week over transferring airline flights from Dulles to National may have been a blessing in disguise. It made the new team at the Department of Transportation painfully aware of the intricacies of the aviation problem that has plagued this city for almost two decades.

The flap began when American Airlines announced that it would, on June 11, start operating five round-trip flights daily between National and Dallas-Fort Worth. This broke the unwritten rule that, with a few exceptions, flights of more than 650 miles should neither originate nor terminate at National. One of American's competitors on the Dallas run, Braniff, matched the move the next day and upped the ante by scheduling a nonstop National-Tulsa ; flight. Pan American then weighed in with three nonstops a day from National to Houston.

Other airlines immediately began considering flights from National to Fort Lauderdale, New Orleans, Kansas City and Denver -- all cities now shut out of the in-town airport. But before they could act, Secretary of Transportation Drew Lewis leaped in with a proposal to make mandatory, at least on a temporary basis, the 650-mile rule.

Secretary Lewis had to do that because the plans of the airlines threatened to eliminate one of the options he may want to include in a permanent operating policy for both National and Dulles. It is, as the history of the last 20 years shows, extremely difficult to move any flights out of National once they are operating there because of the political influence of the passengers who use them.

If National is opened to flights from Dallas, Tulsa and Houston, as the three airlines proposed, it will inevitably be opened to flights from any city that can be served by planes able to land there. Such a move would be disastrous for Dulles; its passenger load would drop further -- and it already had lost 25 percent of its business between 1979 and 1980. And such a move would require either a vast expansion of National or the removal from the airport of short-haul flights from places like Charlotte, Columbus and Buffalo.

The lesson Secretary Lewis and his colleagues should draw from this affair is that a National airport policy for this city cannot be achieved through deregulation and reliance on the good will of the airlines. Their current economic interest lies in maximizing their use of National, regardless of the burden that imposes on the people who live under its flight patterns. Secretary Lewis has a responsibility to protect those citizens with a new policy that systematically forces the transfer of flights and passengers from National to Dulles or Baltimore. If that requires more regulation than this administration is inclined to impose, Mr. Lewis should recommend that the federal government get out of the airport business entirely and turn both those fields over to the state of Virginia.