Okay, Lavos would be erased in all the times he would be in his pocket dimension. So in the saved timeline, the only times Lavos would exist would be his crash, destruction of Zeal, destruction of Magus' castle, and his death in 1999ad. Or at least thats where I place it.
He would be alive before he entered the PD, he would be alive when he destroyed Zeal, because he came out of it, same with Magus's castle, and my theory on his death is that after Crono confronted Lavos, he retreated back into the PD, and fought him there.