Will flashing zip file overwrite existing files?

I have a gapps package for 5.1 and it refuses to flash because gapps already exist on my phone. But the gapps on my phone don't have trusted face. I will modify the gapps with trusted face so it installs even with gapps already on my phone.

I want to know if flashing a zip file with a file that already exists will overwire the existing file with the one in the zip? This is so I know that already existing gapps will be replaced with the new ones.