The editor offers a way to "protect" part of the source to remain untouched while editing or changing views. Just use the "FCKConfig.ProtectedSource.Add" function in the configuration file.
Note that there currently isn't any way to "lock" displayed content in the editor. The content protected with ProtectedSource will actually be invisible during editing. It may be used instead, for example, to protect custom non standard tags or server side scripts. By default, FCKeditor uses it to protect <script> tags from activation during editing.
Example for ASP style server side code:
FCKConfig.ProtectedSource.Add( /<%[\s\S]*?%>/g ) ;
Example for PHP style server side code:
FCKConfig.ProtectedSource.Add( /<\?[\s\S]*?\?>/g ) ;