My drone brood have sunken caps, the worker brood is unaffected, there are no other signs of foulbrood, all bees and larvae appear healthy. All pupa removed from the capped brood are healthy and white. no brown or black colours or ropey goo inside.
I am sending my samples off to the DPI but the samples seem completely healthy. Is there anything else that could cause the Drone brood to have sunken caps?
I’d guess mechanical damage happening when pulling up the frame and elevated drone cells scraping against adjacent comb/box wall 
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Hi Kristy,
A slide test sounds like a sensible precaution.
Sunken cells can often indicate the presence of a disease.
I agree that it does not look like foul brood in this instance, however, sunken cappings are one of the earliest symptoms, so there is also a possibly you may have caught it very early.
Would you please let us know what the DPI comes back with?
Hope you receive good news for your bees.
All the best.
I definitely agree with @Georgina .Drone brood is the first to get damaged while removing brood frames, seeing as it sticks out further. That worker brood on that frame looks perfect to me.
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It came back negative for AFB and EFB, should I just assume it was caused when pulling the frames out of the hive?
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My answer would be “yes”
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Hi Kristy,
I think that’s the answer we were all expecting, but it is reassuring and responsible to have it confirmed - pleased it was a good result for your colony.
Yes I think that is the most likely cause.