Will the programs installed to my HDD be affected if I clean install to my SSD?

Solution
Clean installing completely "uninstalls" all programs even if just doing an in-place reinstall.
If you have games like those from Steam and origin, you will need to transfer them to another disk.

If you are adding another disk to be the new primary, here's the steps:
1) Remove the old disk
2) Put in the ssd
3) Install windows in the new SSD
4) shut down and install the old disk in another port (do not change where the SSD is)
5) When you start up, make sure to select Windows in the SSD
6) Go to the disk manager and remove the boot and recovery partitions from the HDD (do not touch the SSD)
7) After restarting reinstall your programs. Steam and Origin games can be reinstalled simply by running the client EXE from it's current location...
Clean installing completely "uninstalls" all programs even if just doing an in-place reinstall.
If you have games like those from Steam and origin, you will need to transfer them to another disk.

If you are adding another disk to be the new primary, here's the steps:
1) Remove the old disk
2) Put in the ssd
3) Install windows in the new SSD
4) shut down and install the old disk in another port (do not change where the SSD is)
5) When you start up, make sure to select Windows in the SSD
6) Go to the disk manager and remove the boot and recovery partitions from the HDD (do not touch the SSD)
7) After restarting reinstall your programs. Steam and Origin games can be reinstalled simply by running the client EXE from it's current location (in your HDD) and it should reinstall the games without downloading or moving them.
 
Solution
Maybe I'm misunderstanding the question, or maybe basroil is..
Regardless, games and programs that are on a secondary drive will likely have problems
since many games and programs keep settings, saves, etc on the main (C) drive.
You'll also likely have further problems because your Registry that stores even more
info on program locations, etc will be wiped.
 


Nope, you're just misunderstanding my response to the question, which already explained the point of your comment without bringing up things like registry and appdata.

Basically, if you reuse the drive, you need to back up. If you add a new OS drive, you can transfer files after the fact. Both need program reinstalls.