I’d recommend backing your config files up to another location - and with .bak . That way, even if the configs are overwritten, you will still have your previous config. You may also want to test this on a non-production server, so taking a snapshot of your production Nginx Droplet, and then launching a new one on which to test re-installing the custom Nginx build would be a good plan. Alternatively, you could start from scratch with the custom build, and then import your config files.