New Hamsphire Gov. Meldrim Thomson Jr.'s plan to fly all flags on public buildings at half-staff "to memorialize the death of Christ on the first Good Friday" was thwarted yesterday when the Supreme Court voted to preserve a district court judge's order that Thomson rescind his proclamation.

The court announced its 5-to-4 vote yesterday morning only 48 minutes after the last of a flurry of papers - some handwritten - had been filed. Uncertainty over the court's decision kept the flags outside the state buildings in Concord, N.H., going up and down like yo-yos.

When state office buildings opened at 8 a.m., the flags were raised to full staff, then immediately lowered to half staff. When the court's decision was announced the flags were again raised to full staff:

The coutr's action ends a skirmish in what may soon become an important battle over the meaning of the command for separation of church and state in the First Amendemt of the U.S. Constitution.

The order preserved by the court was issued by U.S. District Court Judge Walter Jay Skinner. The 1st U.S. Circuit Court of Appeals overturned it. The Supreme Court stayed the appeals court ruling, thus reinstating Skinner's order.

Skinner left a door open to Thomson. He temporarliy restrained the governor from lowering flags on public buildings on Good Friday "unless before that day" Thomson "shall have issued and publicly disseminated a declaration clearly putting such action in a secular context, without officially endrosing the tenets of Christianity or any other religion."

Thomson did issue a second proclamation, but he did so yesterday morning rather than "before" Good Friday.

The second proclamation declares Good Friday "an appropriate occassion to commemorate the historical impact on western civilzation of the life and teachings of Jesus Christ and the principles of human integrity, dignity and decency which he espoused. . . . Flags flown at half-mast on our buildings will memorialize the contributions of Christ to our society. . . ."

Both declarations end, "I also urge our fellow citizens to fly their own flags at half-mast and their lapel flags in a position of distress on Good Friday."

Late yesterday, Thomson asked the federal court in Boston for permission to lower the flags to half-staff in accord with his second proclamation. Thomson said that if he recieved court approval he would lower the flags today.

Thomson signed the first declaration Tuesday. He had isued basically the same declaration in 1976 and 1977 without drawing complaints. This time, however, five clergymen, represented by the New Hamsphire Civil Liberties Union (CLU) tried to head him off.

On Monday, the CLU petitioned Judge Skinner in Boston (no federal judge is sitting in New Hamsphire, for a temporary restraining order. CLU lawyers I. Michael Winagard and H. Jonathan Meyer argued that the proclamation would inflict "irreparable harm" on the rights of the clergymen under the First Amendment, which forbids law-making "respecting an establishment of religion,"

The harm from lowering the flags would be in the official participation by the state "in the celebration of the Christian holiday of Good Friday, giving grave offense" to the clergymen and other citizens of New Hamsphire, the lawyers said.

Skimer issued the two-part restraining Wednesday noting that the "time frame . . . precludes the luxury of a scholarly dissertation. . . . " Citing a passage in the first proclamation portraying "the moral grandeur and strength of Christianity as the bulwark against the forces of destructive idealolgies" [sic], Skinner said:

"There is not even a pretense of neutrality in this document. It contains all the seeds of divisiveness that the establishment provision was designed to prevent. It not only seeks to advance religion, but a particular religion."

The judge saw "considerable likelihood" that the clergymen "will prevail on the merits" in subsequent litigation and, without a restraining order, "will suffer irreparable harm . . ."

While ordering Thomsom to withdraw the proclamation, he said it would go too far to deny the possibility that a second one might be devised that would be "centered around the life of Jesus," but that still would be "sufficiently devoid of endorsement of Christianity . . . so as not to offend the strictures of the First Amendment."

Both the CLU and Thomson appealed. Circuit Court Judge Bailey Aldrich held a hearing in Boston Wednesday night.

The next day, the appeals court, in an unsigned opinion, said that Skinner had only touched on "legal issues far more complex than the facts;" that he had overlooked the absence of "any excuse or reason" for the clergymen, who knew of the 1976 and 1977 declarations, to delay legal action until Monday; that it "is unfair to the courts to be required to make . . . decisions in haste" on the issues involved, and that Skinner's order, even if correct, puts "a serious burden" on Thomson.

The CLU then came to the Supreme Court where, Thursday night, Justice William J. Brennan Jr. prevented the appeals court from nullifying Skinner's order pending consideration of the matter by all nine justices at a closed meeting starting yesterday at 9:30 a.m.

In handwritten papers filed after the session began, New Hampshire Attorney General David H. Souter and two aides argued that governor issued the second proclamation "at the earliest practical time," that it brings him into compliance with Skinner's order because it recognizes Jesus as "an historical figure" without endrosing Christianity and that it is therefore "secular."

The CLU contended that "clearly established law" prevented them from going to court until they knew Thomson was going to issue the first proclamation. "Had he really wished to issue a secular declaration, he had a whole year to do so," the CLU asserted. It also charged that the second proclamation offends the First Amendment, partly because the manner of Jesus' death it memorializes is "a solemn religious doctrine."

Neither the majority justices nor the dissenters reached the merits of the dispute.

The majority - Justices Brennan, Thurgood Marshall Byron R. White, John Paul Stevens and Harry A. Blackmun - merely stayed the appeals court order pending filing of a petition for full-scale review of the case. The stay expires in 90 days if a petition is not filed, but otherwise remains in effect until the Supreme Court makes a final judgment.

Chief Justice Warren E. Burger dissented, saying that, the second proclamation having been issued, the CLU application to overturn the appeals court "appears to be moot."

Justices Potter Stewart, Lewis F. Powell Jr. and William H. Rehnquist dissented because "we would not disturb the order ofthe Court of Appeals."