It would seem to me that you want to decrease systemic inflammation when you are having an asthma flare so you would want to give her meds on schedule.
That said, I believe that the inflammatory mechanism for asthma is different than for CD so it shouldn't make any difference to her asthma to give her CD meds on schedule.
Be interested to hear what the docs say to do.
Does she have inhaled allergies? When Badger's asthma got worse I always did a painstaking top-down cleaning of his room, washed all bedding and window coverings in hot water and removed anything from the room that couldn't be cleaned like stuffed animals or a rug. He was allergic to dust and dust mites so, even though I kept the room very clean normally, the extra cleaning seemed to help. I always used the covers for the mattress and the pillows and kept an extra set of sheets bagged in plastic so I could swap them out quickly and easily if his asthma flared suddenly.
Hope she feels better soon.