I don't know... I think Tony isn't Tempus and Lois isn't safe yet. He was just a paranoid hotel owner.
Let's see... in the original timeline Lois wouldn't have been feeling sick, so Barry wouldn't have suspected of lead poisoning and wouldn't have gone to the Western Hotel. Both would have been safe.
Tony's actions were a result of Tempus interference in the past (making Lois ill). But I don't think he is Tempus.
And now story has changed, because in the original timeline Tony wouldn't have had reason to threaten Lois and Barry and wouldn't have been arrested. Lois would remember if Tony had been arrested in her past. How will this affect the future?
And Lois isn't sure about Paul anymore. Could this change her future, too?
Oh, and there is no way Lois will not recognize Robert James when she sees Clark in the future.
Okay, my head is spinning so much that it's hurting.