The song is from Beyonce's latest album "Lemonade" and has a strong country influence. Both Beyonce and the Chicks were raised in Texas.
Celebrity gossip site TMZ and Elle reported that the CMAs responded to flack over the performance by scrubbing their social media accounts of any mention of Beyonce or the Dixie Chicks.
Related: Beyonce, Dixie Chicks may have stolen the show at the 50th CMAs
By late afternoon Thursday, the CMAs appeared to pick up on reports claiming that it was clearing the Chicks and Beyonce and re-posted Beyonce's Instagram photo sharing the studio version of her and the Dixie Chicks' performance. A photo was also included in an Instagram collage.
It also shared the Dixie Chicks' Facebook post about the performance after sharing clips and GIFs of performances by Carrie Underwood and Tim McGraw and an all-star tribute to Dolly Parton, among others.
The Dixie Chicks responded with a succinct tweet that included a Soundcloud link to the studio version of their "Daddy Lessons" collaboration with Beyonce.
"If we all turn this up really loud, together we can drown out the hate," the tweet said.
Outspoken lead singer Maines got a little more vocal on her own Twitter page, even quoting Beyonce's song "Formation" in response to the chatter and joking about the CMAs.
In response to the alleged scrubbing controversy, the CMA issued a statement to E! News:
CMA has not erased any mentions of Beyoncé's performance on the CMA Awards. In advance of the broadcast, CMA removed a 5-second promotional clip from ABC.com and CMA's Facebook page. The promo was unapproved and CMA removed it prior to the broadcast. Beyoncé's performance with Dixie Chicks was a highlight of the evening and we are continuing to share the amazing full-length performance clip via our official social channels.