I think this is a bad situation to be in mate, I lost a drone on my main account at 15% damage, my clan mate lost 1 at 20% damage. The game is bugged and seems to be getting worse.
As the admins have not yet answered you, I will tell you exactly what they would say. Email support, explain the situation to them and give them as much information about it as possible. Don't forget to give them your user ID, your ship name and the server you are on.
I managed to get my drone back, my clan mate is still waiting to hear from them after a few days of waiting. So you may have to be patient. But let me know how you get on, good luck