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The incident is making a lot of conservative members' heads spin and marks a shift in the organization's tactics, which appear to be more about procedure than substance, they say.
"The whole thing of trying to tie TPA into Ex-Im, I thought was a little far-fetched," said Rep. Blake Farenthold, a conservative from Texas. "That is actually a reversal of what the Heritage Foundation was speaking a few years back on trade."
Many Republicans, from moderates to conservatives, are scratching their heads as to why Heritage Action would score a free-trade bill negatively.
"It's seems a little illogical to me," said Rep. Steve King, a conservative from Iowa who has been a supporter of Heritage and plans to vote "yes" on TPA. "Don't we know that [Ex-Im bank] is not part of this discussion? It is not part of the TPA. Did I miss something?"
Still, few would discount the impact Heritage Action's "no" vote alert could have on the future of TPA.
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Rep. John Fleming, a member of the conservative Freedom Caucus and one that is still undecided, said Heritage Action's move "alone probably lost some votes for TPA." In what will likely be a tight final tally, those lost votes could make a big difference.
From the beginning, winning over some of the Republican Party's conservatives was a steep climb. Deep distrust in the Obama administration made it hard for Ways and Means Chairman Paul Ryan to make the case to Republicans that a vote for TPA was not a vote of good faith in the president, but instead a vote for congressional empowerment.
"I still don't have confidence in the president, but when we when we talk about Trade Promotion Authority, that authority is Congress's authority. I see it as such," said Republican Rep. Scott Rigell of Virginia.
Ryan and Republican leadership had been working in close communication with outside groups like Heritage to try and ensure they—at the very least—stayed neutral on the bill. When Heritage Action made its announcement, one Republican leadership aide said there was palpable frustration.
(RELATED: Trade Bill in Jeopardy as Democrats Hold Back)
"It is total fiction. No one in this chamber is talking about Ex-Im and trade in the same breath," the aide said. "They have concocted a false pretense to oppose a bill."
Heritage Action says it tried to work closely with Republican leaders, but concluded in the end that they were not willing to make the concessions the group was asking for.
"We have been very clear since May 22 that conservatives should be using this opportunity to leverage TPA and get Boehner and McConnell on the record on Ex-Im," Holler said.
Tom Rooney, a Republican deputy whip, said that while he once relied on the Heritage Foundation's policy papers and leaders when he was a freshman studying up on issues, he's grown tired of many of the outside groups' tactics.