NEI no longer generates a server-side config when installed on a 1.12.2 server, regardless of whether or not there is an NEI folder in the config directory already.

The config should be located in your_server/your_world_name/NEI/server.cfg I can confirm the file is generated in dev.

Thanks for letting me know the new location for the config! It used to be in config/NEI/server.cfg, and I wasn't seeing it there anymore, but I'm glad to know that it still exists.