Hi--
Some people use water soluble glue to tack down the applique pieces, like Roxanne's Glue Baste It. Some others do use the fusible web. I haven't heard about it degrading. Instead of putting fusible on the entire applique piece, some people cut out the center part and just use it to hold the edges.
I am interested in this too, so I googled and found this pdf '
http://digitalcommons.unl.edu/cgi/viewcontent.cgi?article=1000&context=iqscresources' If you skip to the conclusion, it may help you to decide. It depends on how long you expect your embroidery to last.
Carol