I have done that successfully. I did a modified log cabin with a flannel center and cotton surround, with a flannel back. I read that flannels can shrink up to 6% and the cottons were allegedly to shrink about 3% so I washed the flannel only first, then washed the finished product. Came out fine without too much shrinkage etc. The finished quilt lays flat and came out really nice. I see a previous post that says to wash both fabrics - sounds like a good recommendation and I'll try that with my next combo quilt. Good luck!