Felix Console vs filesystem

Question

There is a note in Adobe docs that I see being repeated at few places.  So want to confirm my understanding. Here is the note in Adobe docs -
Start of note
       Saving configuration directly via the Felix Console is stored in the filesystem, not in the repository. This is also the case if a repository-based configuration is modified via the Felix Console: these changes are not saved back into the repository and will not be applied on the next restart of the system.
End of note
Here is the deal - I had configured Day CQ Mail Service through Felix console. It is being used for workflow notification. Since I did it via Felix Console, once I restarted the local instance, I was expecting that the config information will be lost. The config setting for mail service are still there. Here are my questions.
1. So which changes are not saved into the repository and which ones are saved?  When does the configuration changes from Felix get lost?
2.  When they refer to 'changes saved in filesystem only' are they refering to for e.g. in my setup - C:\cq5\author\crx-quickstart ?  In my setup, cq-5.5.0-author-p4502 is located under C:\cq5\author. There is repository, conf and other directories under C:\cq5\author\crx-quickstart. Is it refering to these directory structure when mentioning filesystem?
Thanks!

Answer 1

What version of CQ are you using ? I just created a Blog entry for managing configuration http://www.wemblog.com/2012/10/how-to-work-with-configurations-in-cq.html hopefully it will help.
Yogesh