The financial reform bill wending its way through Congress this month is widely expected to include some form of the Volcker rule that aims to keep banks from making market bets using funds backed by the federal deposit insurance fund.

The announcement of the Volcker plan in January sent bank investors into a funk from which they haven’t recovered.

The shares of the five trading-happy big banks most affected by the proposal  — JPMorgan Chase , Goldman Sachs , Morgan Stanley , Bank of America , and Citi — have together lost $45 billion in market value since then.

But if the big banks aren’t crazy about the Volcker rule, what they really detest is the derivatives ban proposed by Sen. Blanche Lincoln of Arkansas.

The industry has tried to muscle it down, with some support from the administration and even some Democrats in Congress. With weeks to go before Congress sends a final bill to President Obama’s desk, the banks could yet succeed.

Yet with incumbent legislators competing to look tough on rich guys with Bloomberg terminals, even Wall Street’s giant lobbying tab may not be enough to swing the balance against Lincoln.

“We’re not confident it will be taken out,” says one banking industry insider. “Even though very smart policymakers say it should be removed, we’re still here talking about it.”

The banks thought they had Lincoln beat. The proposal — which would separate federally insured banks from their derivatives businesses — has been questioned by the administration, some regulators, and even House Financial Services Committee Chairman Barney Frank, normally not a pal of the banks.

But Lincoln survived last month’s vote on the bill sponsored by Senate Banking Committee Chairman Chris Dodd, D-Conn.

And Dodd, an early skeptic of the proposal, has since indicated that Lincoln’s primary runoff victory this week strengthens her hand. “I will not weaken this bill,” he said Thursday.

Even if it stays in, the Lincoln proposal is no bank-killer. Skeptics say it lacks strong enough enforcement language to make the big banks pay attention, and analysts emphasize that over time the industry will find new ways to mint profits.

“It’s hard to underestimate a bank’s ability to replace lost revenue streams through the evolution of new product/services,” Collins Stewart analyst Todd Hagerman said in a note to clients Thursday.

Still, the banks are looking for a way out. One oft-discussed compromise would swap Lincoln for a stronger Volcker rule. “We believe the door remains open to removing section 106 language on bank derivatives units from the bill,” Concept Capital analyst Jaret Seiberg wrote this week.

In the meantime, bankers also have been trying to weaken the Volcker plan. They want to create exemptions that would let them invest in hedge funds and private equity funds under certain circumstances.

But Volcker last month pronounced himself opposed to any modifications, and legislators are trying to make sure the strong form of the rule actually goes into effect.

A group of U.S. representatives this week sent a letter to Frank urging that the final regulatory reform bill banish the Senate’s call for a two-year study of proprietary trading before any ban goes into effect.

Allowing a government panel to implement the rule after a study “will create needless delay and will likely result in a significantly watered down version of the rule,” a group of representatives led by Maurice Hinchey, D-N.Y., wrote to Frank Wednesday. “For these reasons, it is critical that the Volcker Rule be implemented without delay.”

Few people beyond Lincoln herself are saying that about her bill. But with Wall Street’s polling numbers hovering just above the plague’s, the Lincoln amendment may yet survive to visit the White House.