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I was able to work around this by using the document decryption tool from the original paperless:

$ /usr/bin/python3 /home/paperless/paperless/src/manage.py change_storage_type gpg unencrypted

(Note for anyone that runs into this, there was an error for me at line 96 of the decryption tool, and I had to change it to:

if os.path.isfile(path):
    os.unlink(path)

After this, the reindexing worked!

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Answer selected by jat255
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