When I took my first quilting class the instructor recommended using cotton thread for this reason: fabric used was cotton and the thread would also be cotton and so the same strength as the fabric. Using a poly/cotton thread would be a stronger fiber and could cause it to break the threads of the cotton fabric.
I would agree with Nessie your 95% finished you might as well finish with what you are using, unless you would rather do everything over.
And as writing this it occurs to me if you are making a quilt for a youngster or one you know will be washed often you may want a stronger thread for the quilting so it holds up. (just speculation on my part)
And given the reasoning in our class-if your quilt is mixed fabrics i.e. cottons, poly/cotton and others it wouldn't matter what thread and poly would probably be great in mixed fabrics.
the bottom line its your quilt, do what is best for you.