Google’s John Mueller said on Twitter that it is safe to remove links from you disavow file “if you’ve cleaned up the links & they’ve been reprocessed.”

So first step, make sure the links no longer are there or you are blocking them in some way. And then, make sure Google picked up on that change. Once both of those are done, you can go ahead and remove it from your disavow file.

John Mueller clarified that they links really should be removed before you remove them from the disavow:

None of this is mind blowing really. This is the back and forth we covered in our to disavow or not post-Penguin 4.

Forum discussion at Twitter.