Blowing up the Multiverse and the concept of time won't affect Lucifer at all, see the ending of Nocturne.
"God says, "I am Alpha and Omega." This is the beginning and end, in other words, everything in the world is God's work. Lucifer, the king of the dark, embodies all of the dark side of the world. If creation is the work of God, destruction is the work of Lucifer. The two may be related to each other like personas. So the concept was an intellectual-looking child seeing from the beginning to the end (the future), an old man who views the present in a considerate manner, and, depending on the player's choice, a sinister demon." - Kazuma Kaneko
Lucifer embodies all Chaotic / Dark things in existence, and is also the embodiment of destruction. And his appearances as a both a child and an old man is to represent how he views time.
"Heh... Looks like I've been killed again. I had originally thought that we were superior to you, I am starting to realize that may have been a mistaken assumption on my part. We and you are just...different, that's all. The more I think about it, the more that seems to be the case... It was definitely that way before, but you're the main players in this world. The world may be ours but you are the ones at its core. Are we nothing but supporting characters? Hmm....
Everything has a back and a front. This is true for all matters. You may have thought that you killed YHVH, but on a larger scale, that is just for an instant, a mere blink of an eye. Don't get me wrong, you definitely did kill him, but one could also say that it's impossible to kill him as well. This is the flow of time, the front and the back.
Using YHVH as an example, existences like my own...in a way I always exist, and YHVH also exists everywhere. The end result for this time around...well, let's just say I remain inside you. It feels kind of good here. I think I'll stay here, just for a little bit. Oh, don't worry, I won't be here forever. It'll be just an instant, a mere blink of an eye.
Soon the next main player will appear. And so will I...And also..."
^ Lucifer explaining how he perceives time.