A couple of years back I was running every morning. I had a set route through San Francisco with a loop through the Presidio and a final climb up the Lyon Street stairs. The stairs connect Green Street to Broadway and are steep and tough on knees. After each run I’d get intermittent knee pain, and over time it got worse and worse. It eventually got to the point where my knee would swell and tighten up after every run. In spite of the discomfort I loved the endorphin kick of the run so I kept doing it anyway. It finally got to the point where I decided to see an doctor. It turned out to be a very quick appointment. Here’s how the conversation went:
Me: My knee hurts.
Doc: When does it hurt?
Me: After I run.
Doc: Where do you run?
Me: Through the Presidio and up some steep stairs.
Doc: Hmmm, does your job require you to run?
Me: No, I do it for my own enjoyment.
Doc: Okay, your knee is fixed. Here’s the deal…stop running up stairs and do some other type of exercise like yoga, or swimming. Your knee will be as good as gold.
Me: ?
Doc: Anything else?
Me: Nope…thanks
My knee has been fine ever since. In today’s age of elective surgery, I’m constantly talking to people who are having shoulder operations, hip surgeries or knee surgeries because they refuse to stop a sport they love even though it’s grinding down their body.
Be flexible and kind to your body. You only get one per lifetime. There are lots of gentler ways to stay fit.
markbartels.org 
Like you, I have chosen my exercise in part by figuring out what does not hurt me. That said, sometimes even this exercise gives me a small tweak. When that happens, I stop for the day and do something else (i.e. if I get a tweak in my stomach while doing sit ups, I stop and do squats instead. If I still feel a tweak, I stop for the day). Exercise is a lifetime journey. You can’t win the race on one day but you can lose it. Listen to your body, it speaks clearly.