My interpretation is you don't need the permit anymore.
Inform the airline.
Let the customs guys know you have a firearm when you arrive.
I left my firearms with customs while on my layover, (no baggage agreement with my airlines)
I picked it up and continued on to the next plane.
I did this all while I still required a permit to transit.
I would do everything the same, except apply for the permit.
This permit had nothing to do with customs. It was a Frankfurt requirement.
They have removed it.
Inform the airline.
Let the customs guys know you have a firearm when you arrive.
I left my firearms with customs while on my layover, (no baggage agreement with my airlines)
I picked it up and continued on to the next plane.
I did this all while I still required a permit to transit.
I would do everything the same, except apply for the permit.
This permit had nothing to do with customs. It was a Frankfurt requirement.
They have removed it.
Haven't had a chance to use German since I was in Tanzania in '85 and almost everyone in camp spoke it! The Austrian gent I shard the 2x1 hunt with told a joke to the Austrian PH in German. They both laughed uproariously! 
My wife and I looked at each other with blank stares.
The gent then proceeded to retell the joke in English so my wife and I could also enjoy the kneeslapper that wasn't.
Something got lost in the translation I guess.
