Follow the directions for an oil change completely, and you should not have a full quart of oil remaining in the engine.
-Ride the bike until the oil is up to normal operating temperature, approximately 10 miles.
-Allow the bike to idle on the jiffy stand for two minutes, to allow the oil pump to scavenge as much of the oil in the engine as possible and send it on to the oil tank/pan. Don't rev the engine as that just pumps more oil into the engine.
-Drain the oil and remove the filter. Sit the bike upright after most of the oil has drained to make sure there isn't any hiding in a corner of the oil pan.
When it's done properly, unless you have an oil pump problem that's leaving excessive oil in the crankcase, you should be able to drain all but about 6 to 8 ounces.
BTW, are we absolutely certain that the Dyna calls for 3.5 quarts? I remember my older TC88 Dyna only calling for 3.0 quarts.

It would be a real shame if Harley had a misprint that caused a whole bunch of folks to worry for no reason.
Jerry