Stand the figures in a shallow tray of hot water, just covering the tops of the bases.
Even if the glue is waterproof, this should soften it enough to enable you to pick off as much as you can (the hot water should soften the glue a bit at least).
Then, allow to thoroughly dry, and paint over the base with a couple of good coats of model acrylic paint.
Finally, re-glue and flock, but this time use a non-yellowing glue! You can get non-yellowing PVA glue, but it's normally sold in DIY stores and can be a bit more expensive.
You can also add some white paint to the glue, which will help to prevent it from yellowing as obviously over time.