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.
@Andrew_Isidoro @methode If you've cleaned up the links & they've been reprocessed, you can remove those URLs from the disavow file.
— John Mueller (@JohnMu) October 28, 2016
John Mueller clarified that they links really should be removed before you remove them from the disavow:
@jenstar @Andrew_Isidoro @methode If those links are still live, unnatural, passing PR, & you can't remove them: keep them in the disavow.
— John Mueller (@JohnMu) October 28, 2016
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.