Some hedgies can be litter trained, but it can take a while and you have to be consistent. Put a little litter pan out with something like carefresh, Yesterday's News pellets, or even paper towels, and when he poops somewhere else pick up the poop and put it in the tray so he learns that that's where it's supposed to go.
I always use a bit of vinegar when I wash hedgehog stuff because it gets rid of the odor, but using a lot of vinegar could make their noses unhappy as they have a very strong sense of smell. You could try once or twice to see if it helps, but I'd focus on litter training instead.
We tried litter training...fail! But luckily hedgie seems to go mostly on and under/behind his wheel so replacing a paper towel under his wheel has worked best for us. Also maybe worth mentioning...not sure how old your hedgie is but when Henry was younger he pooped EVERYWHERE and that has since changed. Even if your hedgie is a bit older I would say habits can and will change.
As far as washing fleece liners. I throw everything in the wash. About once a week I do a load of "hedgehog laundry" which include all fleece liners, fleece strips and any hedgie towels. I use a moderate amount of detergent (which happens to be the scent free stuff) and it doesn't seem to bother my hedgie. We are sure to always use the same brand so if he does at all notice the smell it is at least consistent.
I have been trying to litter train him and he seems to use his littler pan about 60% of the time. He is a baby, only 8 weeks old so that might also be why. I'll try placing a paper towel under his wheel, he poops around there a lot. Thanks!