Do you have the grade of bolt and torque specs? Does it have spring washers? They might have a low enough preload or grade that they don't need to be swapped, which is the case sometimes too. God bless that engineer if that's the case because he actually thought about servicing it during the design phase, and didn't resort to high performance bolts to get the forces he needed. I'm not a chipper mechanic studying manufacturer documents during rebuilds and maintenance, but that's why some manufacturers call for it on various types of equipment and why some mechanics do it while working on stuff. I'm not saying you need to swap them everytime, but if it said to do so that's the reason. Are you saying those bolts are original to the machine, the machine that you've run everyday for years and years now? Did you ever once inspect the bolts, and if you did how did you do it? Ever once mic the shaft to see if it's necked down, or dye check it for cracks? Check the thread with a new nut to see if the threads are stretching?
I hate to tell you this, but the people writing the owners manual usually can't wrench on stuff correctly. Depending on what you're working on, you might be expected to know stuff that doesn't come in the instruction manual, and is considered basic mechanical knowledge. An example would be that if you are torquing to an actual value you have to have lubricated threads or the reading is going to be wrong, it's not gonna spell that out to you but to do it right you have to know that. Swapping out hardware kinda fits in that category depending on what it is and how tight they're getting it. I work on all sorts of different stuff, and on different piping systems and equipment we replace bolts every time you have it apart, other times if the threads didn't rust away they're fine, you have to know the difference and when to do each. Head bolts and studs on engines are always swapped too, and it sometimes sucks because they often get stuck in the block so the temptation is to say eff it. But you'll come unglued if that's what causes it to blow up, trashing other parts or causing injury. It sometimes fits in the might as well type of thing too, especially for engine rebuilding, since you are doing it you might as well do it right.
I got a buddy who wrenches on stuff far more than me. He's got a big tub grinder, and i saw he had a pile of bolts and new teeth for it. I asked him how often he changes the bolts and he explained it like this: the old bolt may survive being beat to shit (remember hardened bolts don't like impacts), and it might be fine. Or it can snap off, throwing a chunk of steel thru different shit you now have to fix, and then when you're done you get to try to get the rest of the hardened bolt out of a tapped hole so you can replace it the hard way. For the 200 bucks or whatever it is to swap the bolts he prefers to just do it right and not do that, saving money and time in the long run. It all just depends.