The Reagan administration's plan to reduce the number of commercial flights at Washington's National Airport is expected to move unscathed through today's House-Senate conference on transportation appropriations.

The plan would reduce airline flights from 40 to 37 each hour, allow non-stop flights of up to 1,000 miles from the current 650-mile limit, establish an annual passenger limit of 16 million and set a curfew between 10 p.m. and 7 a.m.

But other transportation issues--affected differently by the two houses' bills--continued to be the subject of intense lobbying yesterday and their fate awaits today's compromise session.

Among them is the future of Amtrak's Cardinal, a train that used to run between Washington and Chicago through Cincinnati and also through the backyard of West Virginia Sen. Robert C. Byrd.

Amtrak discontinued the train Oct. 1 on grounds that daily service would mean a $10.4 million annual loss for the national rail passenger system. "The train is a dog even if it's named for a bird," Amtrak President Alan Boyd recently told the American Council of Railroad Women.

Last week, however, during consideration of the appropriations bill, the Senate by a vote of 75 to 12 bowed to the wishes of the minority leader and required Amtrak to reinstate the train despite the objections of Commerce Committee Chairman Bob Packwood (R-Ore.). Packwood, whose committee has substantive jurisdiction over the railroad industry, objected to the fact that the Senate was "legislating" on an appropriations bill.

Numerous "substantive" changes in the law were made in the appropriations bills on both sides. The House bill, for instance, contains an amendment sponsored by Rep. Elliott Levitas (D-Ga.) that would not allow a Civil Aeronautics Board order to take effect in January.

The order would prohibit U.S. airlines from participating in International Air Transport Association conferences at which the international cartel members set fares on routes across the North Atlantic. The Senate, having been advised by the administration that it opposes the House amendment, did not adopt that provision.

Two other vigorously lobbied provisions to be taken up today also involve the airlines. One involves the amount of subsidy airlines are paid for service to small communities.

The Senate bill would limit payments under one of the subsidy programs to $28 million a year, down from an estimated $69 million this year. The Senate bill would also limit payments under the program to cities boarding fewer than 80 passengers a day.

Another provision could alter significantly the aircraft loan guarantee program that some of the newer, lower-fare airlines like Air Florida and People Express have utilized to buy aircraft for their short-haul services. Lobbyists for USAir, American and Eastern airlines reportedly have been seeking to alter the program in ways to exclude the buyers of McDonnell Douglas DC9s and Boeing 737s on grounds that the loan guarantees give the new airlines an advantage.

The Senate bill would amend the program to limit loan guarantees to the purchase of aircraft with 60 seats or less, an action that would eliminate the users of DC9s and 737s and would concentrate the program on aircraft that could be used solely by the commuter airlines.