NPR reports that the reason why the executive order made by Gov. Youngkin violates federal law is because the order is in violation of the National Voter Registration Act's "quiet period". From Scopes, here is the explanation of the "quiet period":
"...all programs which "systematically remove the names of ineligible voters from the list of ineligible voters" must be completed 90 days before a federal election."
The reasoning behind the lawsuit is best explained in this quote from the article by Assistant U.S. Attorney General Kristin Clarke :
“Congress adopted the National Voter Registration Act’s quiet period restriction to prevent error-prone, eleventh hour efforts that all too often disenfranchise qualified voters,” Assistant U.S. Attorney General Kristen Clarke said in a statement. “The right to vote is the cornerstone of our democracy and the Justice Department will continue to ensure that the rights of qualified voters are protected.”
Overall, the claim is true; that the Department of Justice's lawsuit against Gov. Youngkin's order to begin removing ineligible voters from the voting registry is in violation of federal law.
https://www.snopes.com/fact-check/justice-department-virginia-voting/
https://www.npr.org/2024/10/11/nx-s1-5150774/the-justice-department-says-virginia-is-illegally-striking-voters-off-of-voter-rolls.