1. Some of the cards refer to cancelling a replacement.I assume units brought back from the Destroyed Units box and the Surrendered Units box are replacements.
(Yeah, this is 7.9.)
Are flips replacements? Education? Experience? Fortifications?
No, those all happen during the Flip Step.
2. While the Soviets cannot stack, if they want to bring a replacement unit or reinforcement into an already occupied city during the organization phase, must they remove unit sitting in the city to the shattered box at the end of the organization phase?
Yeah, that's the way I read 8.4.3.