COLUMBIA — Employees of Charleston’s S.C. Sea Grant Consortium will keep their jobs and Charleston-area university projects will move forward after senators Wednesday turned back most of Gov. Nikki Haley’s remaining budget vetoes.

The 20 employees of the Sea Grant Consortium, including 14 full-time state workers, will join the 20 employees from the S.C. Arts Commission in returning to work today.

The workers likely will not get back the pay they missed since the agencies were forced to close more than a week ago following Haley’s vetoes of the agencies’ funding.

That’s because the new fiscal year that began July 1 started just days after the Legislature delivered Haley the budget, a situation Statehouse observers have called unprecedented.

The Sea Grant Consortium uses state and federal money to fund research and education programs on coastal and ocean issues facing South Carolina.

Haley said in her veto messages that the institutions the consortium aids should band together to pursue grant funds themselves rather than the state operating the consortium as a separate agency.

Rick DeVoe, the executive director of the consortium, said he doesn’t blame the Legislature or Haley for the lost pay.

“It’s just the way the situation played out,” he said.

He said lawmakers should learn from it and try to make sure the budget never again gets passed so late in the fiscal year.

Charleston universities also benefitted from the Senate’s votes to override Haley’s vetoes of project spending.

Senators reinstated $2 million for a College of Charleston interactive digital technology project, $200,000 for an upgrade of The Citadel’s Jenkins Hall Arms Room and $5.5 million for the Medical University of South Carolina’s Ashley Tower renovation.

Haley had labeled the projects and others like them inappropriate earmarks, or pork spending.

Senators also overturned the governor’s vetoes of $10 million in one-time money to help fund 2 percent teacher pay raises and $454,000 to help fund nonprofit rape crisis centers.

Senators devoted more time debating Haley’s strike of the use of $10 million from the state’s portion of the National Mortgage Settlement for the S.C. Commerce Department’s Closing Fund than any other veto.

Senators ultimately overturned the veto, sending the money to Commerce.

On Wednesday, Haley called the plan to divert the money away from helping struggling homeowners “morally wrong.”

Senate Democrats supported the governor’s veto, while their Republican colleagues said adding the money to the Closing Fund could help bring jobs that would help those homeowners pay their mortgages.

Charleston GOP Sen. Chip Campsen said the state doesn’t have a reliable and fair method of distributing the money directly back to homeowners.

Thirty-three of Haley’s 81 budget vetoes were upheld during the two-day veto session, reducing state spending by about $4 million from the state’s $6.8 billion combined general fund and capital reserve fund spending plan.

Last year, Haley’s first in office, lawmakers sustained nine of her 35 vetoes.

Haley stood by her budget strikes, saying she will continue to veto the use of one-time money for recurring items.

“I will continue to say it is not my job to win a popularity contest,” she said. “It is my job to strengthen the fiscal health of this state.”

Reach Stephen Largen at 864-641-8172 and follow him on Twitter @stephenlargen.