Question About C.o.a.'s

Yes.

Put them in a polyethylene clip lock bag of appropriate size,
or seal in between clear acetate sheets cut to size, with a tiny piece of tape on each corner, provided you can still fit in the box in which the coin is packaged.

That way, the C.O.A. can be recovered intact.

Some older proof coins were packaged in a velvet lined box, but the coins were not encapsulated. In this case, cover the coin with a clear piece of acetate sheet, loosely laid on top of the coin.

I agree. If you are bothering to keep them, then keep them as original as possible.

Acetate sheets cut to appropriate size may be the best way to go,
because if the C.O.A. is normally included inside the packaging with the coin, such a thin sheet(s) may be all that can be accommodated and have the packaging (box?) continue to be closed properly.