I'm putting in a few fixes to make the quote / angle bracket conversions for #includes work correctly. I was not able to reproduce the conversion overwriting the filename as you described, but the new code is more strict, so it shouldn't have problems like that.
Now, if you have #include "fred.h" just putting your cursor on the quote and typing "<" will convert it to a system-header style angle-bracket include. Conversely, if you have #include <fred.h>, just putting your cursor on the opening quote and typing " will convert it to a nice quoted include.
Common C/C++ misconception: Quoted #include's only look in the current directory or path relative to the current file. In fact, they also search the include path (-I), but they do not search the built-in compiler search path for system headers.
Helpful C++ hint. Use quoted #include's whenever referencing your own headers (as opposed to compiler or third party headers). Then you will be less likely to pick up a like-named system header and the compiler won't fool around searching system directories for #include's that are definitely not what you are looking for.