I am half way through my Junior year and have dropped a solid 5-6 percentage points from hard classes. I want to know if they will factor in my consistent 2 year 98% averages with my so far 92%, or if they look at my junior year and call it a day?
A drop in performance during junior year can be a red flag in the admissions process, but in your case I wouldn't worry too much about it. You're still earning grades in the A range while taking more difficult classes! There's no way colleges will think you decided to slack off or your earlier grades were a fluke.
The difference between the two sets of grades is not significant enough to warrant concern, and most schools will factor in your higher averages from freshman and sophomore year in addition to your junior year grades. Junior year matters the most to colleges, but the other years are also considered.