The bypass_compile_and_fetch_binaries.py script should be updated to parse the etc/evergreen.yml project configuration file both with and without the patch applied. (See the parse_evergreen_file() function.) If the compile_flags expansion for the ${build_variant} build variant has been modified, then compile shouldn't be bypassed.

Note: The git show HEAD:etc/evergreen.yml command can be used to get the version of the project configuration file without the patch applied.