I think you will find that many formulations of epoxy do thicken with age, often the hardener. The jb weld the op is using is a putty so I'm thinking it has a lot of thickeners in it already. I have experienced old epoxy thickening as well but it continued to harden fine. You can also thin it with a small amount of alcohol but that can weaken the final product. Many "wood preservatives" are simply thinned epoxy.