Hours after Scully's Twitter account was deleted following an alleged hacking that took place on Thursday night, Welker's own account was no longer active.
Fox News is told that Welker deactivated her own account and was not asked to by the Commission on Presidential Debates (CPD), according to an NBC source.
Fox News reached out to the CPD and NBC News for comment.
The Scully-moderated presidential debate that was scheduled on October 15 was officially canceled by the CPD after President Trump pulled out of what became a virtual town hall. Biden subsequently withdrew from the debate and has since scheduled an ABC News town hall for the night that the debate was supposed to take place.
The third presidential debate, which is being moderated by Welker, is still set for October 22.
Meanwhile, Scully had been facing controversy over a tweet showing him reaching out to Trump foe Anthony Scaramucci went viral Thursday night.
The "Washington Journal" host appeared to reach out to the former White House communications director, who has become a vocal supporter of Joe Biden, in the now-deleted tweet that read: "@Scaramucci should I respond to trump."
Both the Commission on Presidential Debates (CPD) and C-SPAN have issued statements claiming Scully didn't actually send that tweet.
C-SPAN's statement said Scully "did not originate the tweet" and added that the CPD was investigating the incident "with the help of authorities." In its own statement, CPD said it "it had reported the apparent hack to the FBI and Twitter" as part of its investigation.
Twitter declined to comment when asked to confirm whether or not Scully's account was hacked. Twitter also did not immediately respond to Fox News' inquiry about whether Scully deleted his own account or if Twitter had taken it down as part of a potential investigation.
Scully himself has not publicly commented on the controversy and could not be reached for comment.
Critics who remain skeptical of Scully's "hack" claim dug up old tweets Friday showing him blaming hackers for other tweets that were made on his account.
Frank Fahrenkopf, a co-chairman of the commission, first made the hacking claim to Fox News Radio's "The Brian Kilmeade Show" Friday morning.
"Steve is a man of great integrity, okay?" Fahrenkopf said. "I don't know this question about whether he tweeted something out or not, I do know, and you'll probably pick up on it in a minute, that he was hacked ... Apparently, there's something now that's been on television and the radio saying that he talked to Scaramucci ... He was hacked. It didn't happen."
Scully's initial tweet caused confusion and fury among critics, with many concluding the moderator meant to send his message to Scaramucci privately.
Scaramucci responded by telling Scully: "Ignore. He is having a hard enough time. Some more bad stuff about to go down."
Scaramucci told Kilmeade on Friday that he thought Scully's tweet was real, prompting his own response Thursday night. He also tweeted later Friday that he has taken Scully's hacking claim "at his word," adding, "Let's not cancel anymore [sic] people from our culture for absolutely something like this. It’s insignificant. He is an objective journalist."
Scully's credibility as an unbiased debate moderator was initially questioned after it became known that he previously worked as an intern for then-Sen. Biden and served as a staffer for the late Sen. Ted Kennedy, D-Mass.
During the 2016 campaign, Scully shared a New York Times op-ed headlined, "No, Not Trump, Not Ever."