I would suspect that the small amount of GP, full set of six max five dots is 1080 points , will simply move to whichever char they are on. The phase is open until the timer ends, so in theory, since you deployed a char, if you would increase a level, or ability, it will increase the deployed GP rating, however, if you remove the mods, that char will lose the aforementioned 1080 points, Since the phase is open for all battles, all deployment etc until the timer expires, any changes during the active timer will affect the GP score, positively or negatively. Think similar to raids, and once the timer runs out, then whatever values are in place for the various scoring points are calculated.