They weren't his notes from what I understand. It was Flynn's 302 form, that Agent Pienka filled out after the interview. At least that's what I think this article is about. And all this time Pienka has never been heard from.
But as his legal team goes on offense in the long-running and still unresolved court proceedings, Powell alleged that FBI officials manipulated Flynns FBI 302 a form used by agents to report or summarize interviews. It's not clear who may have done the alleged editing, though ex-FBI agent Peter Strzok was involved in the original interview.
This was an altered form related to one of the FISA applications. So unless there was a FISA on General Flynn, this has nothing to do with the General. That said, it would be the MOAB if there was a FISA on Flynn and this turns out to be his FISA.