You must be using fenders designed to fit 700c wheels, which are a larger diameter than 26" wheels.
I use 26" PB Hardcore fenders (60mm width) with both 26" and 700c wheels, and have no issues fitting up to 26x2.35 (60mm) Big Apples or 700x35 Marathon Supremes or any tires smaller in diameter or width. No need to adjust the fenders at all unless using 26" slicks, and even then, it's only to eliminate the "unsightly" gap between the tire and fender.
Running a 700x23 tire in a 60mm wide fender works fine, but is perhaps not the most aerodynamic setup.