Will seed change?

Ok so yesterday I RNG'd a shiny Kyogre. It was working fine. So then I beat the game and decide to go for latias. Iv RNG latios on Ruby before so it was the same process but on my poke finder the numbers aren't matching the latias at all, so I have battery in my sapphire it's dead,and not soldered on. If it made random contact and with the prongs and say it had a lil juice in it, will it change my seed?? Because I tested the RNG system on a random too just to be sure and none of the numbers and Pokemon are matching on my poke finder list. That's the only thing I can think of that might've happened? Or will mixing records have some effect on the seed and such? Because I also did that yesterday. I'm at a loss here.