Although past Speakers have used such threats routinely, Boehner is personally averse to such bare-knuckle tactics, and his leadership style relies on strong relationships and earned loyalty rather than fear.
Nevertheless, leadership made it clear that lawmakers would face repercussions, including having committee assignments stripped, if they voted against the CR.
But in the end, 48 Republicans including numerous subcommittee chairmen and one full committee chairman defied Boehner's threats and voted against the bill, in part, Republicans said, because they did not believe Boehner would go through with it.
"I don't put any stock in it," Flake said Friday when asked if he was concerned he could lose his position on the Appropriations Committee.
"I might have lost my place on their Christmas card list," said Rep. Jeff Landry (R-La.), who voted against the bill Wednesday and then switched his vote when the bill was brought up again Thursday night. "But, you know, I don't think they would hang me out. ... It doesn't matter. I represent my people."
According to GOP aides, by midweek it had become clear that while Boehner and his team might have hoped they could avoid a nasty standoff, it was exactly that sort of dynamic that had made it possible to corral their extremely conservative Conference on other big-ticket items, and a fight was inevitable.
Boehner convened a closed-door Conference meeting Thursday during which conservatives were able to vent their frustrations. Leaders and more seasoned rank-and-file Members made the case that keeping up the fight might even force them to negotiate with Democrats, leading to a more expensive measure that did not offset disaster spending.
The ploy worked. By the end of the meeting, five of the conservatives who had voted against leadership Wednesday had stood up during the meeting to announce they would switch their votes, and when the chamber voted early Friday morning, more than 20 Republicans switched their votes.
GOP leadership aides acknowledged the process is far from pretty but said that given the makeup of the Conference, allowing conservatives to duke it out for proposals with no chance of passage such as the Cut, Cap and Balance bill this summer or Flake's demand for added cuts in the CR provides the best route forward.
"Managing the psychology of the Conference is really important," a senior GOP aide said. "I'm just not sure we know how to do that yet," the aide acknowledged.
Still, some Republicans lamented the status quo.
"For me, the [CR] debate should be a fairly simple matter. It's a six-week CR. It's trying to keep the government functioning until then. We had an agreed-to number in the Budget Control Act, so we should be able to move appropriately," Rep. Charlie Dent (R-Pa.) said.
"I think it's ill-advised to bring the government to the brink of closure every three months. ... We have a fundamental basic responsibility to affirmatively govern the country," Dent said.
"And the public loses confidence ... in everyone working here in Washington when we fail to meet our most basic responsibilities."