I had a similiar problem with one of my older Ragnarok Server. at one point it does not shown up in the server list, nor dedicated server list, not favorites.
In Steam client it was set under "Server". But no one could find it. Direct connection did not work either.
Till I noticed that the Server Port changed! it was not 27015 anymore. May you check the port settings on your server and in Steam. (unter your user id on the Nitrado server page)