Prednisone is best reserved for emergencies, as it is not really safe. It is possible to have lifelong issues with diabetes after being on prednisone for just a few days, so nobody can tell for sure what it will do for your wife. It's like a roll of the dice. In most cases, prednisone can be used for a few days or even weeks without major side effects.
But Entocort is far safer. She's not taking it three times a day, is she? It's supposed to be taken all at once, just once a day. How long has she been on Entocort? If it has been longer than 8 weeks, then it probably won't help. The Pentasa dosage is low for somebody who is in a flare - the best results are seen at 4.8g but on the other hand, Pentasa is not that effective for most people.
Her best chance of effective medication is using Imuran, a biologic, and/or changing her diet to SCD. If she wants to experiment, she can try LDN.
The word "flare" means different things to different people: what are her symptoms?