Is it actually quilted? If not, I would not submerge. I would spritz the areas with water and let them sit, then gently pull off the glued items. If it's water-based glue, this should work. If it doesn't work, you might consider whether to use something stronger, such as Goo Gone, Goof Off, acetone, or alcohol, or maybe reconsider pulling the appliques off at all.

If it is a washable glue can you just peel the pieces off and re-glue where you want them? I use Roxannes glue baste if all the time , also ELmers school glue sticks. Any marks it leaves come out when I wash it when it i finished.

I once put a Laura Heine creation with Fabric Fuse Glue on a background that was in her kit. I believe the Fabric Fuse is suppose to be permanent. I decided I just couldn't live with the background and was ready to trim around the applique and put it on another background. Well, I tried to gently tug the applique off and it worked! The background still had glue on it where the applique was.

I was able to remove the bears from my quilt very easily. The minute the quilt was submerged in cold water, they literally fell off! So now I can start over usiing Batik!

Had used Aleene's Original Tacky glue, which is water soluble & excellent on fabric. Dries clear.