Since being on LDN, I've done a quick taper with budesonide (a week of 9mg, a week of 6mg, and a final week of 3mg) with my gastroenterologist's blessing. It seemed to work for me, as I experienced what I think was something like a "mini-flare," or perhaps it was the beginning of a flare-up that I caught early, so to speak.
Before I tried LDN, however, my first go round was similar but each round was a month long instead of just a week. (So, one month of 9mg, one month of 6mg, and one month of 3mg.) It seemed to do the trick for me -- my only caveat is that I had a couple of false starts with the drug, as when I was first diagnosed I was supremely depressed, and I was under the impression that the drug was causing it. Because of that, I stopped almost immediately after starting it, but over time I gradually got to the point where I was ready to try it again, and it did what it was supposed to do. I eventually got to a point where I was "good enough" to start trying LDN -- I wasn't 100% after my run with budesonide, but I was definitely doing better than when I was first diagnosed.
I'm not claiming to be an expert, but I would think that using Entocort with LDN would be pretty much OK, and if you did the normal three month course, that might work well for you in terms of getting the flare under control while staying on LDN. I know that staying on corticosteroids isn't exactly the best idea, but I found that Entocort was a lot more manageable and a lot less side-effect-y than Prednisone.