It is possible to have airborne mold spores or other contaminants latch on to the chaff ( even in a window of a couple of hours).
Some growers/breeders prefer "green pods" over "popped pods" because mold spores cannot penetrate the seed pod and this is it easier to keep the seed batch sterile.
A popped pod is not hopeless though, you can still sterilize it to eliminate any potential mold/contaminants.
However, there is also that rare (but potentially troublesome) possibility that a stray orchid seed from another plant has latched onto the chaff of the open pod. This could get mixed into your seed batch and have a duck mixed in with the swans.