Carefully dissect a seed and check for multiple embryos - they will look like thin wavy layers tightly stacked on top of one another inside the seed coat. If there are multiple layers (polyembryonic) the seed will be just like whatever fruit it came out of. If its just a single embryo seed (monoembryonic) it will be a hybrid of the mother tree and whatever pollinated it.
But... changes don't show up in the fruit, they show up in the seedlings grown from the seeds inside the fruit. Can you remember if all the orange-like fruits were on just a few branches in the tree or scattered on the branches in amongst the ponderosa lemons? Hopefully you will say the orange-like fruit was all on different branches because if you don't, we may have to re-write all the books on citrus genetics. I'm going to assume the orange-type fruits really are oranges and that your FIL's tree is grafted onto a sweet orange.
