Thought I'd commented on this before but I guess I was a little distracted at the time with Taffy
I've had them go on their own, and I've had to get them put to sleep... it's never easy. Even when they drive you up the fucking wall and you're ready to wring their necks every time they piss in the middle of the floor or something... it's still a dagger to the feels when it's time to actually end it.
Hope Inca is doing okay... I know animals can get really attached to each other and get pretty upset when their buddies leave them and they don't know why.
It does get better over time, as you come to terms with the fact that you did what you thought was best for them... really, it does.