Hmmm... I've had to deal with nematodes recently. I don't believe they effect the larvae's but I don't know if they effect the pupa.
Can you post a photo so we can get an idea of how many nematodes there are?
1. If nematodes can attack pupa directly, then moving the pupa to an artificial pupa chamber is best.
2. If there aren't a lot of nematodes and we learn that they don't harm pupas, then you can probably leave it as is.
3. If they don't harm pupa, but there are a lot of nematodes, or will be a lot, then moving to an artificial pupa chamber maybe the best.
These are just my thoughts on it. Hope it helps a little!