I tried to recreate the issue to get a better idea of what you’re referring to. Is it that, when you change the blink/smile shapes’ relative key from
Basis to a new key (say,
Basis2), that the blink/smile shape keys are still basing their deformation off of the original
Basis shape key? (Meaning, when you set the values of the blink/smile shape keys to 1.000, the shape reverts back to the way it looks in
Basis without the wrinkles of
In that case, you can fix it by selecting all vertices in the blink/smile shape keys and using the Blend From Shape operator under the W (Specials) menu in Edit Mode, then pressing T or F6 to open the properties, and setting the blending key to
Basis2, Blend value to
1.000 and enabling the Add checkbox. Note that if you don’t move
Basis2 to the very top of the shape key list, you still have to set it to 1.000 to have it show up in the blink/smile shape keys.
As for the add-on, at the moment it doesn’t have a feature that automates this process across multiple shape keys.