Although this is rather an enhancement it would be nice to modify the guarded 
section by first comparing the replacement code until the first difference is 
found (and the same from the end back) and omit the replacement of the possible 
initial (and ending) exactly same part of code.
Example:
existing code:

a();
b();
c();

new code:

a();
b();
d();
c();

the first difference is letter 'd' so the 'a();\nb();\n' would stay untouched. 
When going from the end the 'c();\n' is the same so it would stay untouched.

This way the breakpoints and other bookmarks in the code would stay where they 
are in the guarded section.
The future improvement could be the full diffing of the changes.
I apologize for high priority and defect instead of enhancement but it would be 
nice to implement it soon so that the bookmarks are saved. If it's too 
difficult please lower the priority and turn it to enhancement.
Thanks
Mila