Our guild level 61 airship had lost all amenities too. We had to use TP to get the Lesser Strength and Altar of Devastation back and PP to get the other amenities back.
Since this is a bug affecting all players I wonder how it managed to get past beta testing.
Well, the damage is done. Fortunately the results of the bug can be fixed by repurchasing what's lost so we can still play on and enjoy the expansion. Still, I feel that Turbine should do something to players so they feel well compensated and forget about this mishap. All that's suggested is a 75% discount on 10 goldseal amenities. That's not much. Most amenities were bought with PP and having to pay again for gold seal amenities means you lost real money because of a game bug.
It will be impossible to find who rebought the lost airship amenities and whether turbine points or PP's were used. Therefore you need to have some kind of refund system that can benefit the guild regardless of who lost the PP's. One way of doing it could be to e. g. extend for free all existing airship amenities by 3 weeks when an update is added and servers are down. That should be rather simple to do. You just increase the number of days remaining for each airship amenity on each ship by 21 days.
Since it will be a few days until an update will be run all guilds should be able to get their amenities back so they can benefit from a time extension.
An alternative way could be to double the duration of each airship amenity extension spent before July 14 from 1 to 2 weeks if the current time left on the amenity is less than 1 month. You don't benefit from stocking up because after July 14 you only get 1 week as usual if you use the extension on the amenity. With this method you will on average get 2 weeks free for each amenity you had.