Something I don't understand about Genetic Algorithms
Generally speaking, evolutionary algorithms stop well short of trying to model real biology, and this is one example of something that occurs in nature but not in commonly used evolutionary algorithms.

Instead, we tend to use a system where all individuals have only one value for each gene, and they're all "active". Replication, mutation, and recombination are considered to be atomic operations with no concern given to any intermediate stages. Consider the simplest case of a binary encoding. You might have two parents, A and B, as

A = 0101101001
B = 1001010010


To do crossover, we simply create an offspring by choosing exactly one parent for each bit in the offspring to copy from. We can formalize this a bit with something called a mask -- a bit string where a 1 indicates that we choose the value from A and a 0 indicates we choose from B. Thus, one point crossover might have a mask like

M = 0000001111


with our parents A and B, we would then get a child C as

A = 0101101001
          ^^^^
B = 1001010010
    ^^^^^^
C = 1001011001


So here, the offspring C has gotten copies of the first six genes of parent B and the last four of parent A, but at no point do we consider the process by which chromosomes would be copied in a biological system. We simply allocated a new variable and did a memory copy to instantaneously duplicate parts of the parents. 

If we want to mutate the offspring, we might simply pick a bit at random and flip it. Again, we don't worry about biology here and how mutations actually occur in nature. We just define mutation to be the flipping of a single bit in memory and do it.

One point crossover is about the simplest thing you could do, but essentially all commonly used methods look similar in that the child gets a single value for each position and no explicit notion of binding or connection to the parents is considered. We don't really think of crossover in terms of chromatids -- we just directly copy allele values using some well-defined (but probably not biologically plausible) crossover operator. So there's never any question of which allele values are active -- they all are.