The hypothetical situation I mean is one where your current retina is reprogrammed to switch red and green stimuli, and your memories are edited so that you don't figure it out from inconsistencies, but everything else is left the same.

The fact that there's subconscious cognitive content to red vs. green can be deduced from things like instinctive reactions† to the sight of blood: the brain doesn't check the color against the memory of other blood, it reacts faster than that to to perception. The emotional valence of colors would seem off somehow after a switch, because those don't appear to operate fully through memory, either. Snap judgments of peoples' attractiveness would backfire as your subconscious applied the rule "green tint means sickly" to someone with a healthy complexion.

I don't think you'd be able to consciously articulate what exactly seemed "red" about that green grass, but parts of your mind would be telling you that something's gone wrong, because they're hooked up not just to labels "red" and "green" but to full systems of processing that would be running on suddenly different stimuli.

†Similarly, chimps raised by humans in captivity will still freak out when exposed to a fake snake, because certain patterns have been encoded deep within. There's no reason for such patterns to be raised to the level of conscious knowledge.