When Secretary of State Hillary Clinton signed off on restarting funding to Egypt's military in March, it sparked an immediate outcry on Capitol Hill from those who thought the the United States was giving up leverage to ensure the military rulers saw through on their commitment to relinquishing power to a democratically elected government.

Those fears were realized this past week as Egypt's court forced the dissolution of parliament and the military asserted its powers once again ahead of the weekend's runoff elections.

The court ruling has thrown the future of the transition into question, and now a key senator is warning it could once again throw the $1.3 billion in military aid to Egypt into uncertainty.

"I have made clear to the State Department that, despite the earlier waiver of the conditions I authored, I would not want to see the U.S. government write checks for contracts with Egypt's military under the present uncertain circumstances," Sen. Patrick Leahy, D-Vermont, said in a statement on Friday. Leahy wrote the law that allowed Clinton to approve money for the Egyptian government without certifying that the military government was moving to democratic transition.

At the time of Clinton signing off, a State Department official told CNN's Jill Dougherty that the decision was to help a "strategic partnership" and the State Department would "maintain the flexibility to make adjustments to our Foreign Military Financing program at any time if conditions require it."

Whether the events of the past week will lead to such "adjustments" remains to be seen. But that money is one of the few levers the United States has right now in trying to influence the process, or at the very least express its concern about the potential course of Egypt's transition.

Withholding the money may not change the military's behavior but that is not the real issue for the United States, said Michele Dunne, a Middle East analyst at the Atlantic Council.

"The question is not can we control the behavior of the military in Egypt but the question is do we want to continue to give that level of support that is preventing a democratic transition," Dunne said. "We can't control their actions."

While the money is substantial, the notion that stopping the money would have much effect is "existential," said Middle East analyst Jon Alterman, who is the Zbigniew Brzezinski Chair in Global Security and Geostrategy and also is director of the Middle East Program at the Center for Strategic and International Studies in Washington.

"If the last 18 months have shown anything, it's that the Egyptian military is playing a long game," Alterman told CNN.com's Security Clearance in an e-mail on Sunday.

Still, Alterman noted the U.S. has the ability to assert some influence, as was the case when Egypt cracked down on American non-governmental organizations, and the chairman of the Joint Chiefs of Staff traveled to Egypt in part to discuss the impasse.

"Gen. (Martin) Dempsey went to Egypt to try to free the NGO workers, and they couldn't leave for two months. To Americans it looked like a stick in the eye. Semi-official Egyptians keep telling me that Dempsey ended up getting what he wanted, just not immediately," Alterman said.

The military-to-military ties between the United States and Egypt are among the few non-monetary influences the U.S. has. For years, Egyptian military officers have come to the United States to train, which has created a deep relationship between the two entities. So, after last week's court ruling and the fallout, Secretary of Defense Leon Panetta was quick to call the head of the Egyptian military, Field Marshal Mohamed Hussein Tantawi.

In the call last Friday, Panetta " highlighted the need to move forward expeditiously with Egypt's political transition, including conducting new legislative elections as soon as possible," according to a statement from Pentagon spokesman George Little.

Tantawi, according to the statement, said the Egyptian military was committed to "free and fair " elections and to transferring power to an elected government by July 1.

Clinton said Thursday the U.S. was "engaged with Egypt" but "concerned about recent decrees" by the military that, though temporary, "appear to expand the power of the military to detain civilians and to roll back civil liberties."

"There can be no going back on the democratic transition called for by the Egyptian people. The decisions on specific issues, of course, belong to the Egyptian people and their elected leaders," Clinton told reporters.

There are more extreme measures the United States could take including coordinating with other allies who have significant relationships with Egypt, such as the British, French and Japanese. Also, Egypt is "badly in need" of assistance from the International Monetary Fund and the World Bank, observed Dunne.

"I am not saying the United States should go there now," said Dunne, noting that it would be an extreme for pressure. "That would be a big deal."

But as Dunne noted, it is the Egyptian military, not the United States, that promised democratic reform.

"It's not like we forced this on them," Dunne told Security Clearance.

The money is also part of a grand bargain the United States has with Egypt to guarantee its peace with Israel. With much of the region in turmoil, especially Syria, the U.S. aid is as much an investment in Israeli security as it is in Egyptian reform.

U.S. officials also point out that, when it comes to nations that are weathering the storms of the "Arab Spring," Egypt is "too big to fail," a bellwether for other countries of the region. The Obama administration must tread carefully between pushing Egypt to do the right thing and shoving it into further disorder.