In March, when Boston restaurateur Garrett Harker and his partners shut down their seven restaurants after Massachusetts issued lockdown orders, Harker assumed the closures would be painful but temporary.

Six months later, three of Harker’s restaurants, including the flagship Eastern Standard — once described as the “perfect restaurant” by The Boston Globe’s food critic — remain shuttered. Harker and his landlord for those three restaurants are in a standoff: He can’t afford to pay the six-figure arrears he has accrued while his restaurants remain shut, and the landlord, he said, has refused to grant a deferral or discount.

“We’re probably going to lose money for another year to a year and a half,” Harker said. “It doesn’t work financially to reopen without a new lease.”

Similar sagas are playing out nationwide as Main Street businesses — especially music clubs, gyms, restaurants, bars and others that were forced to close by the coronavirus pandemic — try to figure out how, or if, they can dig out of debt.

Nearly 98,000 businesses have closed permanently since the pandemic took hold, according to an analysis by Yelp. And the fate of many that remain open increasingly hinges on their ability to renegotiate their leases. A recent survey by Alignable, a social network for small-business owners, found that one-quarter of those polled had fallen behind on their rent since the shutdowns began. For those in the fitness and beauty industries, the number rose to nearly 40%.

The problem may worsen now that an initial flood of federal aid has dried up and a sharply divided Congress has been unable to agree on further relief measures. The government’s $525 billion Paycheck Protection Program gave more than 5 million businesses a one-time cash injection to pay workers and other expenses, including rent, but most recipients have now spent the money.

“For 10 weeks, our revenue went to zero and stayed at zero,” said Rhonda Stark, the owner of three Orangetheory Fitness gyms in Ohio that were shut down from mid-March until late May. Stark’s collective rent bill, her largest fixed expense, tops $32,000 a month. She hasn’t paid it in full since March. Although she got PPP loans ranging from $45,000 to $75,000 for each of her gyms, most of it went toward payroll, as the loan rules required. Stark’s gyms have reopened at a reduced capacity, cutting her sales by about 30%. To stay open, she needs to strike new deals with her landlords.

Retail rent collections plunged in April to just 54% of the total owed, according to Datex Property Solutions, a software company that tracks data on thousands of its clients’ retail properties nationwide. By August, collections had rebounded to nearly 80%, but some tenants — like movie theaters, clothing retailers, hair salons and gyms — were much further behind.

“When tenants can’t pay the rent, it imperils landlords’ ability to pay their own overhead and their loans, and the whole thing cascades,” said Mark Sigal, chief executive of Datex.

For both sides, it’s a complicated dance. Property owners have their own expenses to pay, including taxes, insurance, mortgage or debt payments and maintenance bills. Buildings owned by real estate investment trusts or Wall Street bondholders have complex management structures and governing covenants that can limit the property manager’s ability to make a deal.

Lance Osborne, president of Osborne Capital Group, owns a retail plaza in Copley, Ohio, that houses four businesses, including one of Stark’s gyms. His company has around 150 retail tenants, and he estimates that half have sought rent relief or other concessions.

“Every one has to be handled on a case-by-case basis; no two tenant cases are the same,” Osborne said. “We’ve always dealt in good faith to try to keep the tenants open and operating. It’s always worth keeping someone, but it has to be an equitable deal.”

Eight of his tenants have declared bankruptcy or are on the brink, Osborne said. He has sued one business — which he described as open and thriving — for nonpayment. For others, he’s gradually negotiating new deals.

Many of those arrangements are informal and fragile. Stark said she hadn’t signed anything establishing new terms for any of her gyms, which means her landlords could at any time declare her in default and crack down. But so far, they have been willing to take it month by month, collecting some rent and verbally assuring her that they’ll keep working with her.

“It’s very tentative,” Stark said. “You call them up, you talk to them about what’s going on. I’ve sent screenshots of my numbers so they can see where we stand.”

But not all landlords are willing, or able, to take a haircut. Oren Molovinsky closed his restaurant Farmboy, in Chandler, Arizona, in mid-July for what he intended to be a short break. He hadn’t paid his full rent for months, but he had reached out to his landlord, the Falls Investors, hoping to discuss options. Instead, he got a letter in late July telling him payment in full was due in five days. When he missed that deadline, his landlord locked him out.

“We were surprised they wouldn’t respond to us at all; my attorney didn’t even get a response,” Molovinsky said.

The Falls Investors sued Molovinsky last month in an Arizona state court, seeking at least $110,000 for what the complaint said was unpaid rent. Molovinsky has told his staff and customers that Farmboy, which sold sandwiches and salads using locally sourced ingredients, will not reopen. (A lawyer for the Falls Investors said the landlord has done workouts with other tenants but chose not to for Molovinsky because he was already behind on his rent before the pandemic. Molovinsky, who acknowledged his arrears, said he had a verbal agreement on a repayment plan with one of the group’s principals, who died last year.)

Harker fears that Eastern Standard — his first restaurant and the only one of his ventures that he owns outright — will soon join that list.

The brasserie opened 15 years ago and quickly gained a reputation as one of Boston’s best spots for relaxed hospitality and cocktails. It sits in a retail space within the Hotel Commonwealth that has changed hands twice since Eastern Standard opened. The current owner, UrbanMeritage, promotes Harker’s “award-winning restaurants” and the foot traffic they bring to the area in a brochure it created to advertise a nearby vacant storefront.

But Harker said he could not afford to reopen unless UrbanMeritage renegotiated his lease, which has a bit more than two years left on it. He has $1.6 million in PPP loans for Eastern Standard and the two other shuttered restaurants — the Hawthorne and the Island Creek Oyster Bar — sitting untouched in a bank account. He plans to return the loans soon if he can’t make a deal.

Michael Jammen, a principal of UrbanMeritage, disputed Harker’s claim that his company was unwilling to negotiate, saying via email that it has “offered multiple discount opportunities both on his existing lease and on a lease renewal” in recent years. Those discussions have continued during the pandemic, Jammen said.

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