Hey sprockets,
This may be a good primer for you on saving templates as text files. Also, have a look at this part of the CP since it’ll show you which of the two (the database version or the file version) is the most up-to-date.
If the file’s edits are more recent that the database version of the template, the system will use the file version to render the page, but it doesn’t actually sync up the file and the database versions.
If you go to edit a template in the CP and see the message you noted above, that means the file version is more recent (and that’s what it’s showing you in the CP’s template editor). Whether the database version or file version of the template is the most recent, however, saving the template in the CP always saves to both the database and the file (assuming you have Save Templates to Text Files enabled).
Does that help explain things a bit?