These sound like good observations.
To explain to you the exact way to do what you want, I would need more details of exactly what you want to do. The flipping gives you low pass and high pass filters, but they are not conjugates of each other. You can't combine them to reproduce the original image. If this is what you want, you should create your own mask for removing the information from the FFT. You can invert the mask to switch between low pass and high pass.
Another option is to copy the FFT image, do the filtering, then subtract the filtered FFT image from the original FFT image to get the conjugate.
Bruce
Bruce Ammons
Ammons Engineering