Since my engineer changed my shear wall spec's, I need to change a 2X4 sill plate to a 3X4 (or 4X4) dimension. My problem is that all the anchor bolts and hold-downs are in place along with an installed cripple wall. My thought was to add wood epox to the existing 2X4 sill plate to get to the required 3 or 4X dimension. Since the hardened wood epox will be stonger than the original wood it should be acceptable. Will this work ?

You should get your engineers approval to do this so you have a record of it in case something happens.

Amircca correct that you should get engineer approval no matter what you do. My suggestion would be to get connecting nuts, cut existing bolts off at half the length of the connection nuts, install the connecting nuts, then install threaded rod to extend the length of the anchor bolts. Weather or not this is do able depends on the size of the anchor bolts which dictates the length of the connecting nuts. I would think the engineer would want the anchor bolts to extend completely through the sill plates. He's not likely to approve your "home made" laminated beam.