Well, since I finished up testing for this last night. I'll post it now. This is about what really is done with all the modifiers when there is a Critical Hit in G/S. If you don't want to read my rant, skip to the Summary at the end.
There are a couple of different explanations floating around as to what happens to the modifiers during a CH in G/S. The most commonly accepted one is that this rinky-dink little Motorola Z-80 is able to perform enough calculations, in roughly the same time as it takes to calculate damage normally, in order to determine which specific modifiers to keep and which ones to ignore in order for the CH to do the most damage possible.
This is wrong.
What prompted the check of this was an e-mail to spunman and myself from White Cat. He had info from Fanha on another possibility of how CHs work in G/S. Where Fanha got the info from, I don't know. Fanha obviously didn't test it, since it was partially wrong. Since he made the GSBot, it undoubtedly handles CHs incorrectly.
I never saw any response from spunman, but I assume he's been on vacation during this time. Since part of the information that was passed on seemed like a much more likely implementation for CHs (and I had never performed any testing on CHs in G/S up until that point), I performed some initial testing. It showed that some basic cases of the part that turned out to be correct worked. White Cat then performed some testing for the other needed cases to insure that the correct part held.
The part that was confirmed by this testing was that modifiers are not selectively ignored for a CH. Either all modifiers are retained or they are all ignored. If retaining them will yield higher damage than ignoring all of them, then they are all retained.
This only applies to stat modifiers, however. I tested for other moves that affect damage calculation. Light Screen and Reflect were tested because apparently Fanha thought these were among the moves whose effects would be ignored or retained based on getting the most damage. They turned out to not be a part of it. Rain Dance and Sunny Day are also not considered or changed during a CH.
Basically, other moves whose effects affect damage calculation will all be retained during the calculation for CH.
During a CH, stat modifications on the two pokemon are checked. If retaining all of the stat modifications on both pokemon will yield more damage than ignoring all stat modifications on both pokemon, then all stat modifications will be retained during the CH damage calculation.
Any other moves whose effects affect damage calculation (such as Light Screen, Reflect, Rain Dance, Sunny Day), whether increasing or decreasing, will be retained for the CH damage calculation.