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Executing gpg -K --with-keygrip returns one key entry. However the private-keys-v1.d directory has two entries. I assume that one of them belongs to a secret key that has been deleted/removed.

Is there any way of restoring a secret key from this directory?

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The question is based on the wrong assumption that for each PGP pair there is one and only one entry in the private-keys-v1.d directory. The private-keys-v1.d directory comprises the key store of the gpg-agent so apart from the private keys used by gpg there may exist other keys used by SSH or X.509 or secret subkeys.

Deleted keys are not going to be present in this directory. On the other hand if you have at hand the private-keys-v1.d directory it is possible to restore the keys as explained here.

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