The rule of thumb that I've heard for herbs in general is to cut stems back by no more than 1/4 to 1/3 of their length. That said, I've cut new growth back a lot further than that on oregano, and my thymes often die back nearly to the ground in winter and sprout out new growth in spring. If it got hot right after you cut them back, that might have stressed them and set them back.
A lot of my plants are barely "hanging on" after this hot summer, but I think (hope!) most will come back stronger than ever next spring.
