Now, though, a legal wild card has been injected into his case and those of several other defendants in California and Washington State.

 

In December, in a little-publicized amendment to the 2015 appropriations bill that one legal scholar called a “buried land mine,” Congress barred the Justice Department from spending any money to prevent states from “implementing their own state laws that authorize the use, distribution, possession or cultivation of medical marijuana.”

 

In the most advanced test of the law yet, Mr. Lynch’s lawyers have asked the Ninth Circuit Court of Appeals to “direct the D.O.J. to cease spending funds on the case.” In a filing last month, they argued that by continuing to work on his prosecution, federal prosecutors “would be committing criminal acts.”

 

But the Justice Department asserts that the amendment does not undercut its power to enforce federal drug law. It says that the amendment only bars federal agencies from interfering with state efforts to carry out medical marijuana laws, and that it does not preclude criminal prosecutions for violations of the Controlled Substances Act.

 

With the new challenge raised in several cases, federal judges will have to weigh in soon, opening a new arena in a legal field already rife with contradiction. Currently, 23 states plus the District of Columbia permit medical marijuana. Four states allow recreational sales as well.

 

“If any court, especially the Ninth Circuit, declares that the provision precludes federal prosecution of state-compliant individuals, this will be huge,” said Douglas A. Berman, a law professor at Ohio State University and editor of the Marijuana Law, Policy & Reform blog.

 

Such a ruling could put federal courts in the odd position of determining “when a state actor is complying with state law,” said Mr. Berman, who used the metaphor of a buried land mine.

 

In Mr. Lynch’s case, prosecutors have urged the appeals court to put off considering the issue until the hearing on his criminal appeal and sentence, which is not likely until late this year at the earliest, but also indicated that they would not back down.

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In a March brief, Mr. Lynch’s federal public defender, Alexandra W. Yates, wrote that any delay would mean “the Department of Justice’s illegal actions, and their chilling effects on California’s medical marijuana system, would continue unabated.”

 

Some also call the government’s quest for delay a cynical ploy as officials wait to see whether Congress renews the provision in the next fiscal year.

 

The California sponsors of the December amendment, including Representatives Sam Farr and Barbara Lee, both Democrats, and Representative Dana Rohrabacher, a Republican, say it was clearly intended to curb individual prosecutions and have accused the Justice Department of violating its spirit and substance.

 

“If federal prosecutors are engaged in legal action against those involved with medical marijuana in a state that has made it legal, then they are the ones who are the lawbreakers,” Mr. Rohrabacher said.

 

Mr. Farr said, “For the feds to come in and take this hard-line approach in a state with years of experience in regulating medical marijuana is disruptive and disrespectful.”

 

The sponsors said they were planning how to renew the spending prohibition next year.

 

The amendment aside, federal prosecutions of state-approved dispensaries have declined sharply in the last two years, particularly since the Justice Department issued a nonbinding “guidance” to prosecutors in 2013. That guidance recommended against pursuing dispensaries, growers and patients who comply with state law, have no links to cartels or interstate smuggling, and do not sell to minors.

 

New raids on state-approved dispensaries have largely ended, said Steph Sherer, executive director of Americans for Safe Access, a private group that lobbied for the December amendment.

 

At the same time, she said, federal prosecutors have relentlessly pursued existing cases like Mr. Lynch’s and an effort to shut down the large Harborside dispensary in Oakland, Calif. Unbridgeable policy conflicts remain; two of Mr. Lynch’s five felony counts were for selling to customers who were over 18, as California permits, but under 21, as federal law forbids.

 

At Mr. Lynch’s 2008 trial, even the term “medical marijuana” was largely forbidden, as was testimony about Mr. Lynch’s compliance with California law.

 

Mr. Lynch opened his business after a decade working in computer software, and he was doing well enough to buy a modest house with an ocean view. He felt excited to be “on the leading edge of a new industry,” he recalled the other day. He had a personal interest, too, having discovered that marijuana eased his severe migraines far better than prescription painkillers had.

 

Janice Peters, who served three terms as mayor of Morro Bay, criticized his prosecution.

 

“He is such a soft-spoken, nice guy, and to tear his life apart just makes no sense,” she said. When the dispensary opened, she gave out her card to neighboring businesses and asked them to report any problems. “There was never any complaint,” she said.

 

Given federal law, Mr. Lynch’s 2008 conviction was no surprise. But at his sentencing, Judge George H. Wu of Federal District Court in Los Angeles recounted Mr. Lynch’s efforts to obey local law and said there was no evidence he had known of infractions federal agents described: that a worker had made secret sales on the side and that some of his more than 2,000 enrolled customers had received prescriptions on fraudulent pretexts.

 

“Individuals such as Lynch are caught in the middle of the shifting positions of government authorities,” Judge Wu said as he disregarded the federal request for a mandatory five-year term but said he felt legally compelled to sentence Mr. Lynch to a year and a day.

 

Once Mr. Lynch appealed, the federal government revived its demand for a five-year sentence and also asked the appeals court to remove Judge Wu from the case in any future proceedings.

 

After Mr. Lynch’s arrest and the seizure of his funds, his family mustered resources for a bond, but he spent nine months and 10 days under house arrest with an ankle bracelet. Unable to find work, he lost his house. For the last year and a half, he has been allowed to stay with his family in this rural area next to the Navajo reservation.

 

“I have no work and no money, and I’m depending on others to survive,” he said.

 

While he waits, he spends his days tinkering on the trailer, repairing fences and practicing oldies on the electric guitar for a one-man band act he developed.

 

His face came alive as he played “Paint It Black,” accompanied by computer-controlled bass, drums and flashing lights.

 

“I love to play,” he said, “but only on days when I feel good about myself.”

 

However, some local bar owners, he said, fearing involvement with a convicted drug felon, have declined his offers to perform.

 

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