The point behind running or exercise in general isn’t to become invincible. Life is hard and exercise is hard, but we have to learn to overcome. Life will throw shots at you. Runs will have nasty hills pop up in front of you. Walks will sometimes seem like they are never going to end. All of that is normal, all of that is what actually makes you stronger mentally and physically.
You have reached a great place when you get to a point where moving forward with your goals is more important to than letting life or circumstances stop you. You have reached a place that shows your mind is focused, clear and ready. Your body is now going to start answering to you instead of you letting tired muscles be in control.
We all have to get over some kind of hurdle. Mine was, or maybe still is, hills. I hate running up hills. My legs get weak and for the longest time I would stop and let them recover. I eventually decided that to reach my goals I had to stop letting my legs be in control on the hills. Once that decision was made I figured out that although my legs did get tired, they actually recovered really quick if I just kept going. The break wasn’t necessary to recover, just getting up the hill was all the was needed.
I don’t know what your hurdle may be, but I assure you that it is at least 80% mental. You will take hits to your confidence with any change to your routine, but keep your eye on the goal and learn to keep moving forward.