Oh sorry to hear your LO is poorly. Bronchiolitis is horrible, mine was in hospital 4 nights when he was around 10 months old.
You have to do what you have to do. It can take some time to recover, even when they seem to be over the worst it can still take a bit of time to really get back to being themselves, mine had to have night feeds for the first time in months so that he could regain the calories lost during his illness.
You will get back on track though.
I always say that an independent sleeper will return to independence either on their own or with a little guidance and support to remind them - they already have the confidence to do it.
I would wait until she is properly recovered or when you feel she can try for a cot nap - and when you are ready too.
Then remind her, I would think that you wouldn't really need much PUPD, possible a little but with more reassurance in the cot rather than heaps of picking up, and I can't imagine it taking as long as it did the first time either.
For now it sounds normal to me that the routine is off track and I imagine she needs lots of extra cuddles, possibly more feeds too.
Try to take care of yourself in all this, it is hard having two young LOs especially with illness in the house. Your DH might be at work but perhaps he can pick up a bit extra house work so that you don't have all that to deal with on top of two poorly LOs?