well as the name says, i believe Killy and Sana-Kan have a past.
as we know Safeguards have personalities and goal of themselves, but they sometimes have to forsake parts or all of, their personality to perform the extermination tasks at hand. in book 3 when Sana-Kan shows that she is not a little kid but actually a Safeguad, she has a battle with Killy, and if you look on her expressions she looks kinda happy to be able to have a fight with him, when she stomps on his face and starts shooting things she looks kinda sad, and then she gets shot through the head she looks really sad and looks at killy saying: "Killy...", then she scans him and says: "Are only your functions restored?" i believe this is a question if he remembers her or not, and she does look sad when he doesn't.
also, when she turns from kid to Safeguard she kills everyone around her without hurting Killy, same goes when she sprouts her wings and flies away, and in the battle she could absolutely decimate Killy, i think this is because she(her personality) didn't want to hurt her old friend or even lover.
further on, when Killy is being rebuilt, he has a vision of 3 people standing on a cliff, i believe they are Killy, Sana-kan and a unknown other, maybe Musubi(was that her name?) from NOiSE. being trained to be special Safeguard agents. The Authority can use these special train Safeguard agents as they please, like they do with Sana-Kan.
and Killy has had a few more punches/stomps/shots to the head, than he should be able to take, so its not weird he doesn't remember anything.
so are Killy and Sana-Kan old friends/lovers? (Y/N)

I'm sorry but I don't think we can realistically speak of a relationship between the two.. Of course they've met each other before or even known each other. But I fidn it hard to believe that this "relationship" goes beyond comradeship or rivalship.

Sanakan: You don't remember?
Killy: No Sana-chan, I don't want to remember.
Sanakan: *cries while simultaneously killing stuff*

Killy and Sanakan might...MIGHT have brushed elbows in the past. But there's nothing between them, not even a hint.

Now Dhomo and Pcell, there's an intriguing pair. I say there's a reason he paused before blasting at her and I bet it happened during the 250 years they spent scrapping it out. Maybe it even involves Dhomo's mysterious vial and the Coelacanth (kinky)

Hell, Blame Academy in its wild exaggeration blatantly confirms that Dhomo and Pcell had something goin' on.

TL;DR
Dhomo x Pcell are my OTP omigawwwwwwww

I guess we'll never really know, will we?

Who cares? Those buildings were cool, and even cooler when they exploded.