I was playing a solo game just now and an interesting situation happened. I had taken out one broodlord in the genestealer lair location, but the other one had an insta-kill swarm surrounding him and was just chewing through my remaining marines. Then I get the event "temporary sanctuary" which reads as follows:

Instinct: Choose a swarm of Genestealers. Shuffle all cards from the chosen swarn into the smallest blip pile.

So naturally, I choose the pile that has been chewing through my battle brothers, but now I have a connundrum. The rules for the broodlord state that it is never shuffled into a blip pile (italics theirs), so what is the proper way to play this out?

What I ended up doing is shuffling in the swarm and leaving the broodlord in place, and then just continued with the spawning as normal. Still ended up being a big enough swarm on him to take me out. I'm not sure if this is the right way or not though.

Thoughts?

I think you did it right. Shuffle everything but BL back, continue on with resolving the card.

I concur. I'd do exactly as you did.