The default setting of GnuPG are quite reasonable but often you will want to make changes to further improve the security and usability, one good reason to do this is to ensure your keys are in the newer pubring.kbx format rather than the pubring.gpg, it is still compatible but using the new format is recommended.
Firstly you want to export all your keys including secret keys, to do this run the following commands.
gpg --export --armor > pubkeys gpg --export-secret-keys --armor > seckeys
Once this is done delete the contents of your GnuPG home folder, typically ~/.gnupg/ or GNUPGHOME, you may want to keep your trustdb.gpg and configuration files.
Ensure the private-keys-v1.d folder exists otherwise you will get an error when importing the secret keys, import all your keys in to the new keyring.
gpg --import pubkeys gpg --import seckeys
If you did not keep your trustdb.gpg make sure you run the following:
Recommended GnuPG Settings
GnuPG has a huge number of settings which you can adjust, but these are the most important ones I recommend adding to your gpg.conf
expert - Expert mode gives you much more control, a must if you want to generate ECC keys s2k-digest-algo SHA256 This sets the digest algorithm to SHA256 rather than the less secure SHA1 default-key (your key id) - Sets the default key which is a good idea ask-cert-level - Asks for certification level when signing a key (recommended)