Former Scottish National Party MP Natalie McGarry alleged Rowling had supported those abusing women on the site.
However, while McGarry appeared to row back on her comments on Thursday night, she also began re-tweeting those continuing to make allegations towards Rowling.
JK Rowling and Edinburgh East MP Natalie McGarry
After an hour-long exchange in which the author demanded firm evidence of McGarry's claims, the MP wrote: "On reflection, I do apologise for any misguided inference that you support misogyny or abuse instead of the folk you tweet."
Rowling had accepted the MP's apology, writing: "Thank you very much, Natalie, and I'd like to ask anyone following me who is being less than polite to you to stop."
However, the author has since questioned the McGarry's motives.
McGarry, who resigned the SNP whip in November but continues to sit in the Commons, had alleged Rowling had re-tweeted support for someone the Edinburgh East MP claimed to be a troll.
Within seconds, Rowling responded to McGarry's accusation, writing: "I'd love an explanation".
The accusation prompted a fiery exchange of messages, with McGarry naming a user on the site alleging their status as a 'troll' was well known - and proof Rowling supported such accounts.
Rowling ended the exchange with an ultimatum.
Rowling quipped that she had a "small island" of lawyers at hand.
McGarry's resignation from the whip in November came after Daily Record and Guardian investigations found that £30,000 due to her Women for Independence campaign was allegedly unaccounted for.
Ms McGarry denies any wrongdoing.