I've seen many tutorials for repairing quilts. One thing to make sure of is that the fabric you replace the squares with matches the style of the other fabrics used. It might help to visit a vintage or second hand store to get old print patterns from clothing or something.
This is all that I seem able to find this morning.
http://www.mccallsquilting.com/legacy/vintage_article06/A lot of article mention that it might be easier to find someone who repairs quilts professionally.
Oh I missed the part where you said the squares are still attached. I'd just hand sew them back in?