Serato - FLAC - and the CDJ 2000s

the file types that serato plays is irrelevant to the 2000's, the 2000's simply control serato, not pass their audio through the 2000

As BriChi has commented, you can certainly play the FLAC files in Serato as the software is handling the file processing. The CDJ2000 is only acting as a controller, it does not have to analyse the file so it is 'removed' from the equation.