re:
So my primary phone is a Lumia 1020. I recently made a purchase in the app store for Puzzle Quest 2. I was excited to see this app in the Windows 10 store (on desktop), but it does not exist there. I'm assuming its because it is not a "universal app". My question is what happens to all my awesome WP8.1 apps when W10Mobile comes out? Will those apps disappear as well? Will Windows 10 Store have different apps on Phone and Desktop? I know they are trying to be "universal", but will developers have the option to keep apps strictly Desktop or Phone?
Very good question.
Obviously, once W10M is "officially" out, W8.1's lifespan will be limited, and support will end at some point (maybe someone can fill in those details from MS).
Regardless of the app updates from W8.1 to W10M, will MS provide updates, firmware, app updates, etc. to keep the L1020 at its best? I doubt it.
My expectation with my L1020, which I mainly use for photos and photography apps (Lumia apps, etc.) and fun stuff, will likely forever remain on W8.1.
I suggest that you keep routine backups of your L1020, in the event you need to reset and want to reload.