The immunogenicity of Cre recombinase is very sensitive to the PFA fixation. I usually reduce the time from overnight at cold to one to four hours depend on the size of brains. You may also try to fix the tissue on ice and reduce the concentration from 4% to 2%.
I do not have experience in this breeding. But I believe you will be using transgenic Col2a1-cre. There will be no homozygosity or heterozygosity of cre. Either cre will be present or absent.