Hi Wren,
Do you have the ID of your original kitty on the pedigree page?
Because if your kitty shows a different eye color there might have been made a mistake and yes this could effect your kitties genetics.
Hopefully you see your kitty listed in your pedigree overview and this way you can trace it's ID.
With this ID I would file an other support ticket explaining what happend and with the right ID included.
I hope this helps some.
Good luck
