I've done some further investigations. I just couldn't get this to work for a while, then I went into trial and error mode.
1. I reinstalled the VPS with Ubuntu 15.04, updated it, generated SSL's with LetsEncrypt and then used your one-click installer.
2. After the install had completed, I checked documents and it works (using the server IP).
3. I then tried to connect using the DNS name, I checked documents and it works.
4. I moved the cert files into /app/onlyoffice/CommunityServer(DocumentServer)/data/certs
5. I tried visiting DNS name via https, it didn't work. Attached the CommunityServer container which warmed up mono and reloaded nginx, https now worked.
6. Tested documents after SSL being enabled on community server and they worked.
7. Attached document server container, restarted nginx, documents still worked via https.
8. Rebooted host server.
9. No longer able to access https, attached community container, restarted nginx, community now loads but documents no longer work.
What am I missing here? What am I breaking?