As Crazybeck mentioned it might be tensions spots. I had them twice but once really bad and it took me over 6 months to get rid of them. There are lots of creams without prescription you can get at the pharmacies which will help you ease the pain and itching (if it's tensions spots) cortisone cream reduces inflammation or hydrocortisone (a synthetic steroid sold under various names) can relieve itching and skin irritation.
It might be an allergie to adhesive as well.
The right think to do would be to take the extensions off,but not knowing what caused what you call blisters (chemical exposure,infection,burning..) it's hard to decide what would be the best path to take. Surely if you take them out you'd have to use different solution like oils rather than acetone based products.Hope more experience geeks will be able to help you!
aleksandra