I've always assumed that Mount Gundabad, like Moria later, was conquered by Orcs. Possibly it became depopulated as a result of Dwarves moving southward to the rich mines of Moria and so was relatively easy prey. I seem to recall something about it being a 'holy' site for the Dwarves and it's occupation fiercely resented.
I assume they got it back sometime in the Fourth Age.
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