What happens when you had something set manually but then disable it on a running server? It depends on the version you're running. Let's say your postgresql.conf file started with the following setting active:
checkpoint_timeout = 5min
You now edit the file to comment that setting out:
#checkpoint_timeout = 5min
Then you tell the server to re-read the configuration file:
$ pg_ctl reload
#checkpoint_timeout is a sighup context setting. The reload command throws a note in the log file.
LOG: received SIGHUP, reloading configuration files
LOG: parameter checkpoint_timeout removed from configuration file,
reset to default
You can confirm the setting using the SHOW command.
postgres=# SHOW checkpoint_timeout;
checkpoint_timeout
--------------------
5min
(1 row)
This behavior is both complicated and version-dependent. Experienced PostgreSQL administrators will usually double-check parameters they intended to change afterwards using the SHOW statement, or by looking at pg_settings, to make sure the settings match what was expected.
Another complicated area here is that it's possible to include additional configuration files from inside the master postgresql.conf. These effectively work as if you'd inserted the text of the file into the spot you included it in. You can see the file's settings originated from using pg_settings in this case, along with what line the active version came from. Also note that if you set a parameter more than once, only the last setting will be registered.