Well basically it depends on what you are training for and how you are training.
Different training lengths and different training styles will use different fuel methods. It is quite a vague question in a way because you aren't asking about a specific training.
If you are training for strength, well you can be training for a while actually if you take proper rest intervals between sets. Some strength sessions can last hours for competitive strongman given the correct rest intervals and length.
Training for endurance, then yes after a point your fuel sources, CNS effects, basic "chemistry" will alter. However, if you are training for endurance you need these things to occur.
Where people get in trouble is they will go heavy at it lifting weight after weight with little breaks for 45-60 mins, then hop on the treadmill and jog for 25 mins and then go to some jumping jack and etc... Is this a problem? If they are training to gain mass or to lose fat or gain strength or preserve muscle mass, yes it is. You have to train for what your goal is. When you know what your goal is you need to then understand how the body works with that goal. Numbers of set/reps and rest times aren't just thrown out there for the hell of it, there are reasons due to your bodies response that there are guidelines for different goals.
So find your goal and figure out your guideline.