Yes, replace in files with regex will do this
Make sure you have "use advanced regexes" checked in editor settings.
Link to syntax is in my sig. Use \n where n is an integer corresponding to your unnamed groups in the replace string. I never got around to adding support for substituting named groups in C::B (but maybe someone else did)
Something like this (untested)
#if WXCHECK_VERSION\(2\s*,9,\s*0\).*?\n(.*?)#else.*?#endif.*?\n
replace with
Edit: placement of spacing.