I honestly don't think there are any hard feelings between the two. They just need to recover from being used as child soldiers in the CA Arc. I also wouldn't say a rift formed. Killua more than anyone understood that Gon was suffering immensely and finally broke after what happened to Kite. His feelings got hurt once because Gon lashed out once. That doesn't negate all the good Gon has done for him and definitely didn't cause a rift.

I think they separated because Killua 1. Felt immensely guilty for Alluka's situation and wants to make up for lost time 2. Wanted to protect Alluka from Illumi 3. Wanted to protect Gon from Illumi's potential pursuit.

I think if anything they need some personal growth. Both have cripplingly low self worth, which contributed largely to the breakdown in communication in the CA Arc. This causes them to recklessly throw their lives away (Gon in particular) and consider their lives as worth less than another's (Killua in particular). They just need some time to mature and then come back.

I think they just need to come back and show their growth to one another and everything will be fine. Killua will hopefully will get better at communicating and stop hiding things from Gon. And Gon will hopefully become less reckless and more perceptive of how his actions affect others.