I migrated an NGINX reverse proxy server with many letsencrypt certificates on it. It's a largely undocumented task, and there wasn't really much good tooling for it. I needed a tool to handle the creation of all the symlinks, and it felt like a fairly nuanced situation, but seeing as some people here are encountering the same issue, I thought I would share my tool with the community.
Enjoy!
Great that you've developed a tool to help others with possible problems!
One question though: why not just migrate the symlinks with the rest? zip has the --symlinks option (short version -y) to do this for example 
Example:
osiris@erazer tmp $ zip -ry foo.zip foo
adding: foo/ (stored 0%)
adding: foo/bar/ (stored 0%)
adding: foo/baz (stored 0%)
osiris@erazer tmp $ mkdir bar && cd bar
osiris@erazer bar $ unzip ../foo.zip
Archive: ../foo.zip
creating: foo/
creating: foo/bar/
linking: foo/baz -> bar
finishing deferred symbolic links:
foo/baz -> bar
osiris@erazer bar $
Also note that if I read your script correctly, it makes absolute symbolic links instead of the relative ones generated by Certbot itself. Maybe throw in some os.path.relpath() magic? -> made a PR for this.
I didn't know that the symlinks were relative. In fact, I didn't know symlinks could be relative. That's super cool and basically makes my tool obsolete. Still, sweet solution. I'll see if I can add this info to the readme of the repository so that people looking can reference it.