How do you collect coins PDS sets where some are only available in special sets (ex: Jefferson Nickels - 1997P Matte Proof)?

My question is general but I'm wondering how people keep their collections when some of the coins are only available in sets. For example, I keep a Jefferson nickel collection in carboard coin flips (for UNC varieties), Saflips (for proofs and more expensive varieties), and in the original cellophane from the mint sets. All of these are in binders with polyethylene 2x2 pocket pages. For the proofs, of course, someone pulled them out of the sets, so I repackaged them in the Saflips (heat sealed). But for some varieties, like the 1997P Matte Proof, they were only available in special sets (Botanic Garden Coin and Currency Set). What I'm doing is putting a card in the pocket page slot that says "See Botanic Garden and Currency Set." I have the set but I don't want to pull the nickel out of it. But now, my nickel collection has cards in it for some years (maybe special sets or ones that may be in slabs). For the 1994P Matte Proof, I did just buy an extra for the collection and also have the set. But the 1997P is more expensive and I haven't done so yet. Also, the earlier proofs are generally in slabs, so they won't fit in the 2x2 pockets either.

I have the same question on other sets too (Kennedy halves special and in slabs, Peace dollars in slabs, SBA dollars, etc,) and I am wondering what other people do. I suppose people will tell me that it is my collection and I can do whatever I want :)

Incidentally, on the 1997 Botanic Garden set, I've read that the packaging has destroyed the nickel. I looked at my set, and the nickel looks OK. So my thought is that if it has not degenerated in 24 years, it'll probably be OK. What is the real story on that? Should I take it out and put it in a heat sealed Saflip?

usually people leave it in the original packaging but if the packaging is harmful ,they send it to a grading service for encapsulation

noteworthy examples include the proof Chinese pandas .they were packaged in pvc and thus collectors send them in for grading