The factory image for a phone includes the current (at the time the image was burned) version of whatever bloatware the carrier installs. From there, the Play Store updates the version to keep it current (unless you have disabled it). An OS upgrade simply replaces (or, in this case, removes) the original version of the app. If you have accepted an update to the app, removing an old version from the factory image will not uninstall the new version of the app.
Net result: Nothing will be forcibly removed from your phone. The only difference now is that if you go to uninstall the app, you will get the prompt "do you want to remove this" and you will actually be able to remove it. If the app was still on the factory image, then you would get the "do you want to uninstall all updates and revert to the default version" and you will not actually be able to uninstall it, only go back to the version that is baked into the firmware.