Apparently signaling an easing of concern over the presence of Libyan and "other known terrorists" here, the Reagan administration's top African expert today pledged continued aid and praised hard-pressed Sudan's efforts to return to democratic rule.

Chester A. Crocker, assistant secretary of state for African affairs, told reporters that the United States was "watching with profound concern" the democratic changes here since the overthrow last April of President Jaafar Nimeri, a long-time U.S. ally.

Crocker was speaking during a one-day visit in which he conferred with Gen. Abdel Rahman Swar-Dahab, head of the ruling transitional military council, civilian Prime Minister Gizzuli Daffa-Allah and other officials.

Observers attached more importance to Crocker's brief presence here -- seen as an attempt to end misunderstandings -- than to his formal remarks or the message he brought from President Reagan.

The administration had begun to display increasing irritation with the transitional regime and the way it was ruling Africa's biggest country, which now is faced with civil war, the aftermath of famine, economic crisis and impending general elections.

Bilateral relations reached a low point Nov. 20 when the State Department urged Americans not to travel to Khartoum because the capital had become a base for Libyan and other "known terrorists" said to represent "possible threats to American interests."

Libyans flocked into Khartoum following the restoration of diplomatic relations, which had been cut years earlier by Nimeri.

Forty-five American officials and dependents -- approximately 10 percent of the mission staff -- were reassigned and a further cut was planned. About 1,000 Americans live in Sudan, roughly split between the capital area and the provinces.

Most of those who left work for the U.S. Agency for International Development, which runs the biggest aid program in black Africa here, and the Office of Military Cooperation, which maintains an aid program with the Sudanese armed forces.

Although the travel advisory remains in force for Khartoum -- it was issued in January 1984 for the embattled south, where civil war is raging -- American officials cited progress recently on several bilateral issues.

Last month, Foreign Minister Ibrahim Ayoub Taha told reporters that six or seven "undesirable elements" had been asked to leave. All those expelled were believed to be Libyans. Taha's remarks remain the only public Sudanese official admission of the U.S. charges, otherwise stoutly denied by Sudanese officials.

Among those returning to Libya was the recently appointed manager here of the Libyan Arab Airlines, whom western intelligence identified as a major figure in the Libyan diplomatic mission in London in 1984 when gunfire from there killed a policewoman.

The continuing travel advisory apparently reflects persistent U.S. concern about the growing number of Libyans in the capital despite recently increased Sudanese surveillance as a result of the U.S. complaints.

Diplomats say they are convinced that the publicized U.S. complaint about security in Khartoum did take a toll in short-term relations between Washington and Sudan.

"But things are looking up," a western diplomat said, noting the change in mood here in the past six weeks.

A shooting incident outside the Palestine Liberation Organization headquarters involving an American oil company worker and Palestinian guards also upset the United States and other western embassies.

U.S. nerves had been set on edge, too, by anti-American statements at the start of the trial of former vice president Omar Tayeb, charged with taking a $2 million bribe for allowing Ethiopian Jews to be flown from Sudan to Israel in 1984 and 1985.

Further contributing to U.S., other western and Egyptian uneasiness over Libyan inroads here was the transitional regime's dismantling of Nimeri's dreaded security apparatus.

Coupled with a still ill-defined military accord with Libya, the disappearance of expert surveillance heightened fears that the vulnerable transitional regime might be veering away from its traditional western and Egyptian supporters.

The transitional regime has defended its renewal of diplomatic ties with Libya by arguing that Khartoum had to improve relations with its neighbors, especially Libya and Ethiopia, if it hoped to end the two-year-old civil war in the south.

Although western diplomats are still concerned about the apparently largely uncontrolled number of Libyans in the capital area, the Libyans have had problems of their own here.

Diplomats report little coordination between the classic diplomatic activities of the Libyan mission, the intelligence agents and the Sudanese revolutionary committees, which are based on the Libyan model of grass-roots governing units.

The committees' leader, Abdallah Zacharia, was under virtual house arrest last month by his followers apparently because of a financial dispute.