This was an obvious question, thanks for the replies.
New flashing installed over the old. You need to do the same thing at chimneys and pipes. But honestly, if this is something you need to ask you probably shouldn’t be charging someone money to do this job as it’s a very basic question.
This roof is also too warn out for a roof over imo.
That is reprehensible to roof over the top of that. That is the exact roof you DONT do a recover on.