The N% weakest genomes are culled without being allowed to reproduce.* From the remainder, everyone is in principle allowed to reproduce, although fitter genomes are more likely to be randomly selected.
Once selected, the breeding genome will pick a partner from the remaining population based on genomic distance. I.e. it doesn’t care much about the fitness of its partner, it just cares that the gene values are close to but not too close to itself (too close is incestuous, too far is zoöphilic, neither being healthy).
Then, at the end of all the breeding, the K% weakest individuals in the current generation are compared to the K% fittest individuals from the previous generation and swapped out if they perform worse. If K% and the population size are both small, rounding may cause zero individuals to carry over from one generation to the next.
inbreeding option controls what percent similarity is considered attractive as a mate, the
maintain value is K%.
Do note that Galapagos keeps a full record of all genomes+fitnesses and it will never create a new genome which is identical to one that occurred before. Especially if the total possible number of different genomes (i.e. a small number of slider, each with only a small number of possible states) is low, you’ll get some weird effects over time as patently unfit genomes are computed anyway, because all the good ones have already been done.
* Although looking at the interface, N is either a constant or may even be hard-coded to zero. I don’t remember whether the bias towards fitter genomes is the only bias left in the most recent version.