How video page flipping works
That sort of problem is what DMA is for. 

When you finish rendering buffer 1 wait until it starts being read out onto the video output, then kick off a DMA copy transfer to buffer 2, you can start doing your mods to buffer two as long as you stay behind the line the DMA core is copying, then wait for VBI interrupt and do the same thing going back the other way. Memory to Memory DMA transfers are generally quick and do not tie up the processor.

Depending on the hardware, reading video ram while it is being displayed is seldom a problem, it is writes you want to avoid (And even there you can just contrive to write behind the line the video hardware is outputting). 

You can even do effects by playing with the video readout DMA addresses between each line, the gameboy for example did this to great effect.