The downside to Aqua Seal and similar mixing mediums is that it creates a patina, both on the product you use it on and on the brush itself. You can easily isolate the problem on a product (as shown demonstrated in my Naked Basics Crave), by only using it on a little bit of the pan, but the makeup brushes pose a larger problem.
A hardened brush can be easily remedied with a little olive oil. I soak the end of a small angled brush in a 1/4 tsp of olive oil for about 5 minutes while I am washing my other brushes. After a few minutes, I massage the oil into the bristles of the brush to soften them up and dissolve the remaining Aqua Seal. Once the bristles are softened, you can wash the brush as usual. I really like diluted Dr. Bronner's lavender liquid soap because it breaks up product really well.
Once you learn how to clean makeup brushes hardened by Aqua Seal or mixing mediums, the product is pleasure to use and I highly recommend it. Let me know how you fix this issue in the comments!