I've noticed that just before mars is conjunct mars, I feel down & exhausted. My mars is in pisces in the 3rd (Koch houses). Lately I had transiting saturn opposite my mars and for two weeks I felt physically miserable and down. Flu symptoms all the way, but not bad enough to stay in bed.
I cannot remember illness while mars transited my 6th, at least not this year. But I do remember a series of illnesses while I had jupiter transits. Very odd. I have no planets in the 6th. Jupiter is conjunct my ascendant in cap.

You could be right.

I was looking at the chart of someone who was quite sick at one point and mars wasn't in H6 but it was tightly aspecting significant H6 planets.

I wonder what it means, though.
Is it misdirected drive or physical energy? or a process of strengthening the immune system through making it go into battle or maybe a call to strengthen the immune system or pay? possibly mars associated with H6 points to a time to pay attention to one's physical energy levels and health ... ?

fighting off colds and stuff - sometimes it can be like a battle. It takes conditioning, preparation and things like that to survive.