What is an "embedded function"? Do you mean a "nested" function? What happens if you set a breakpoint where you want it?
Do you have a clear all in your code, which deletes all breakpoints? If so, and if you do not want to avoid debugging in general, remove the clear all. It is a painful junk at all when written to functions or scripts, while I see many users, who call it cleanly from the command line.
A hard-coded breakpoint is inserting a keyboard command. While this is bullet-proof and not impressed by clearing, it is less convenient, because you have to care for a clean removal of these lines for the productive code. But applying changes to the code after debugging is a bad programming practice in general, because any modification could add a new bug and therefore an exhaustive testing must follow afterwards again...
