Ok, I managed to solve the issue. Thanks for all the input.
I found the root of the problem.
When I initially created the certificate, I used a non-official docker certbot image to issue the initial certificates.
I used deliverous/certbot instead of the certbot/certbot image. Then, when I tried to renew the certificate, it placed the renewed certificates in a -0001 suffix folder.
I confirmed this by issuing new certificates using the --staging flag on the deliverous/certbot image, and then proceeded by attempting to renew the certificates using the certbot/certbot image, and then got the -0001 suffix folder.
I then deleted everything and issued new certificates using the certbot/certbot image, and renewed using the certbot/certbot image, and everything worked fine.
There were obviously differences in how the certificates were created with the deliverous/certbot image.
From now on, I’ll stick to the official certbot images.