The Fairfax County Board of Supervisors, worried that it may have unintentionally doomed a Metro bond referendum on today's ballot, yesterday agreed to pay the transit system $6.3 million it had withheld and to reaffirm its support for the referendum.

The supervisors voted 8 to 0, with one member absent, to send Metro the county's quarterly contribution. Four weeks earlier the board had withheld the payment by the same margin to protest Metro's refusal to increase its fares.

The board's vote yesterday came a day before county voters will decide whether to approve $25 million in bonds to continue paying Fairfax's share of Metrorail construction. The supervisors all support the referendum, despite a history of rocky relations with the transit authority.

"I've been very concerned that some of the citizens have been getting mixed signals from the board," said Supervisor Marie Travesky, a Republican from the Springfield district. "I hope it's not too late, because we want to get the message out that we support the 101-mile system as we always have."

Travesky, who supported the board's vote to withhold funds last month, said she believed some supervisors' anti-Metro statements had damaged the referendum's chances. In an apparent reference to Board Chairman John F. Herrity, a fellow Republican whose style she often criticizes, Travesky added: "There were lots of other statements made by at least one member of our board that we weren't going to ever make that payment, or at least not until Metro shaped up, whatever that means."

Herrity said yesterday he does not know whether the board's actions will affect today's vote, but he did not moderate his criticism of Metro's management.

"We were not going to stand by and be held up by them and have our budget be thrown out of whack by their inept operation," Herrity said. "We didn't get exactly what we wanted, which was a fare increase, but the bottom line is the same."

Metro originally promised area governments it would raise fares on Jan. 1, but backed off because of fears the increase would lead to further declines in ridership. When the Metro board of directors, including Fairfax Supervisor Joseph Alexander, postponed the increase until April or July, Fairfax officials calculated the delay would force them to pay about $520,000 extra in subsidies.

The supervisors then voted to withhold their regular quarterly payment until Metro changed its position on the fare rise. That didn't happen, but the transit authority did offer its member governments assurances they would not be responsible for providing the lost revenue.

The board's earlier vote to withhold funds came on the same day it approved the creation of its own bus system to replace some Metro routes south of Alexandria, an action that some said contributed to the appearance of a lack of confidence in Metro. The county still plans to operate its own buses around the Huntington Metro Station, which is expected to open in late 1983.

The $25 million Metro bond referendum is thought by some politicians to have less of a constituency in Fairfax than a $25 million road bond question, which is being pushed by the County Chamber of Commerce, or the $58 million park referendum, championed by the county's formidable "Green Team" lobby.

The League of Women Voters assumed responsibility for pushing the Metro referendum, and league president Leslie Byrne said yesterday she believes most voters understand that the referendum is for construction, while the supervisors' complaints concerned operating funds. Byrne also said the county is committed to pay for the construction out of general tax revenues if the referendum fails.

"It's got to be paid for," Byrne said. "This is something that we contracted for."

All three bond issues are being opposed by the Fairfax Taxpayers Alliance on grounds that the county is already deeply in debt and that the bonds would increase real estate taxes in the county