It's always difficult picking with the same object however if you change it to 1 when touching the green it does mean it's different. A second variable might also be useful to differentiate it from the others to work out what's happening.
One way is to use system pick nth instance 0 and 1 in the overlap of red and red. You might be able to compare 0th instance where variable changed and then pick 1th instance and change that variable.
Another way that is to put red sprite in a family. Then when you change the red sprite that is touching green to 1. You can say if family where var=1 (the red sprite) is overlapping red, then change red. This successfully picks the other red sprite as the first one was picked as family.
They are the two ways I know of to do this.