I had exactly the same thing happen. I cut my low intensity cardio way down (was doing pretty much HIIT only), and my HDL went down about 12 points; my LDL and Triglycerides went up, and too much for my liking. I'm doing a few things differently as a direct result:
I am taking a Niacin supplement as an experiment (reaserch this, and if you try it, I suggest a NOFLUSH version, in case like me you're one of the 35% that gets a flush from regular niacin).
I am increasing my low intensity cardio again, but still doing a lot of HIIT, too.
Here's some of my thoughts as to why:
Low intensity cardio uses fat (and muscle) for energy. The fat comes from several places, including the Triglycerides and LDL in the blood (used as a source for fat-fuel). Thus, as the Tri's and LDL are burned-off, the HDL has less work to do (a primary role is binding with, then transporting oxidized LDL to the liver for burning).
Thus HDL increases in the blood. When you stop using the blood-based Triglycerides for fuel (i.e, when you do HIIT only, including heavy-weight strength training) then HDL goes down accordingly, as it is now swamped with LDL that's not getting burned off in high-intensity exercises or post-workout recovery to the same extent as low intensity cardio.
Do you follow my line of thought here; and does it seem reasonable? That's my thoughts on the matter.
I also have another more worrying thought about this: I followed the almost universal advice last year of taking high GI carbs/protein as a post-workout meal. My concern is an errosion of insulin sensitivity as a result of the massive blood-sugar spike. This in turn drives up Tri's and LDL, and reduces HDL.
This is a completely different mechanism to the one above, but in my mind, both seem plausible.
Insulin resistance is not unheard of in bodybuilding (but I also know it's not that widespread either). So in addition to my elevated cardio work (with more low intensity stuff - walking and such), I am also not taking high GI carbs period; not even after a workout.
My primary goal is getting my blood in excellent condition, and a secondary goal is building muscle / looking good.
I have tried to run this by a nutritional expert but not had much success. I intend to pay John Beradi's consultancy fee in March or so (christmas bills now...) and get an hour of his time on this subject, coz to me it's really important in the great health and fitness scheme of things. Once I've so-consulted, I'll see if John lets me make a public posting on his views.
I still believe fish oil helps; but I think it's better for joints and fat-mobilization than for reducing LDL. For me, low intenstiy cardio worked SPECTACULARLY for reducing LDL/Tri's, so I am not especially surprised at my recent reversal, given that I stopped doing the low intensity stuff to help promote muscle growth/retention.
I'm trying a different strategy to the one that I KNOW will work, because I don;t especially relish the prospect of losing 20LB or so of muscle on the treadmill again.