I believe you just need to add this: personal-digest-preferences SHA256 cert-digest-algo SHA256 default-preference-list SHA512 SHA384 SHA256 SHA224 AES256 AES192 AES CAST5 ZLIB BZIP2 ZIP Uncompressed
To your .gnupg/gpg.conf where the files are being signed.
Fixed
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Link on the subject:
https://juliank.wordpress.com/2016/03/14/dropping-sha-1-support-in-apt/