I forgot about this but actually bad news. voicemail.confis the configuration for voicemail (it’s not generated from the database). So if you lost it, you’re probably going to have to redo voicemail from scratch.
Just a side comment: this seems weirdly inconsistent with the way the rest of FreePBX generally works.
The other confs that comes to mind are asterisk.conf and modules.conf. I don’t think freepbx does anything to asterisk.conf and it just edits modules.conf in place but this makes sense because you don’t want to rely on FreePBX config for the very basic startup of asterisk.
If I recall, at one point in Asterisk pre-history, voicemail.conf did not allow #includes, so all config (generated and custom) had to be in the single file. That limitation may no longer exist, but FreePBX has not been changed.
Another one that comes to mind is manager.conf. FreePBX can read/write out details for the admin user, but otherwise does not touch the rest of that file.