I hear and feel your frustration! Some projects just don't go well, some of my current success as a quilter come from the past 40 years of bad stuff... Did the border itself disintegrate or was it just the flannel? I'd just cut it off at the stitching line and restitch, using a 1/2" on the flannel side. Typically any seams on the back should be 1/2" and pressed open anyway.
Too warm depends on your local... being an ex-Alaskan and current soggy Seattle-ite I always use batting with flannel but I personally hate working with flannel so avoid it when I can. Last year though I did a crib sized donation project with a flannel back (and batting) which reconfirmed to me that I just don't want to deal with it.
Sometimes I use flannel instead of batting. There is still hope for future projects with the rejected backings.