The mountain ringlet is only found high in the remote and hard to reach Cumbrian peaks.
The instrument from Mardale had been feared destroyed, according to the auction house.
Auctioneers say the instrument was used in Mardale's church before the village was flooded in 1939.
The damaged charity box was discovered at Mardale Head during training, the team says.
A chair rescued from Mardale church has been in Rachael Heyman's family for more than 80 years.
Stories from Cumbria include swimmers being warned after harmful algae is found in Windermere.
