I assume that you have setup an override directory for your copy of these files. I would locate this directory and FTP the files to your PC and look at them with an editor or notepad and see if your changes are contained in them. If they are, then for some reason your override is not being used. Check which template you are using, naming etc.

Normally the admin will not allow saving if you are not editing an override, and will only load an editable file from the template override that you have specified. The admin will indicate the path of the file loaded, check that path also.