If you look at this little picture and consider the original Flex V1 to be at the point the two lines cross, then increasing to TOGA is the same as moving downwards into the "Whatever" zone.
When You flex you reduce the thrust to match the space available. As you reduce the thrust the range of V1 that would allow a safe outcome reduces. If you can reduce all the way until you become runway limited then you are at the point where the lines cross and you only have one V1 available. But that V1 is always within the usable range for higher thrust settings.
Vr and V2 are essentially based on weight (stall speed) and the only reason you might get different values with different types of calculation (rated / flex) is down to the engineering selection of Vr/V2/Vs ratio. For our flex calculation with added thrust the original Vr and V2 are still valid.