Remember seeing a YouTube video years ago showing a weight lifter in decent shape, who continued his weight lifting but focussed on long distance running. The way his body changed shape was actually quite alarming, he couldn't maintain the muscle mass and ended up looking a bit skinny fat. Was shown on these forums afaik.
D.P I've noticed you saying quite a few times that HIIT carries a much higher risk of injury. Sure, I agree to an extent. But you're making it sound as dangerous as doing the cha cha cha across a mine field. HIIT can be done on a cross trainer, rower, treadmill, whatever. These are all relatively safe pieces of equipment to do HIIT on, anyone who is going to be massively prone to injury during HIIT, is probably going to be at risk walking to the shop
Of course if you run you will loose upper body mass if you don't training for it, there is a very simple reason, every 1lb of body mass increases your marathon time by 2 minutes, which is pretty huge. Muscles also require increased blood flow and consume blood sugars and oxygen, all of which is pretty bad if you want to run fast. Which is why all the pros go to great extremes to loose upper body mass through calorie deficit and very careful core strength excises etc.
If you want to have a lot of upper body muscle while doing lots of steady state running then that is no problem, because steady-state running releases Testosterone and Human Growth Hormone which both increases muscle recovery and development.
Just look at Triatheletes that need upper body strength for swimming, they are all very ripped. And I can also speak form experience, doing up to 10 hours of steady-sate running a week and little swimming by upper body has never been so well toned and defined, far more so than when I was keenly doing weights. In fact i am quite alarmed at how fast my upper body muscles are developing now I have started swimming. This may be due to the fact that my regular running is icnreaisng Testosterone and HGH that increase muscle development.
A particular rigorous exercise will release Cortisol, a stress hormone which in consistent high amounts has some negative outcomes (weakens immune system for starters). But steady-state running for 60-90 minutes doesn't increase cortisol levels, HILT does because it is a very extreme exercise. Very long endurance running, a marathon runners weekly long run (2-4 hours) will increase cortisol in moderate amounts, partly why runners only do long runs once a week. But increasing cortisol over a short term is not a big deal, so there are no real health risks from HILT or long runs due to that.
As for thyroid function, again no issues at all from steady-state cardio. the same can't be said for HILT unfortunately. 12 hours after exercise T3 levels were LOWER than the steady-state runners:
http://www.ncbi.nlm.nih.gov/pubmed/22450344
To put it bluntly, the internet has several bogus pseudo-science claptrap about steady-state running and thyroid issues that are not backed up by science. In fact, the science is clearly in the opposite direction. 30 seconds on Google will quickly disprove the nonsense from.