Whenever you change a attribute through the web gui or by the command file, nagios saves the changed attribute in its retention file (Depending on your retention settings). When the attribute has been marked as changed, nagios will ignore any changes in the config file for this attribute.
notifications are enabled for a particular host
someone disables notifications for this host and reenables it later on
another guy changes the notifications setting in the config file for this host and wonders why the changes will be ignored
With the modfied attributes filter a list of host and services can be created which have modified attributes. And they can be reset by a quick command or by a normal host/service command.
Nagios will then use the settings from the config file on the next reload.