Hi Marek, currently all of my projects run "standalone", which I interpreted to mean that a copy of the KSDK will be copied into my project folder and used for builds. It's this local copy that I had modified. So if I understand what you're saying, this dialog appears because the installed KSDK does not match the local copy, and therefore I need to make the change to the KSDK folder as well.
If this is correct, this will work fine because the intent was to eventually change the projects to use a linked folder anyway (back to the KSDK installation folder). However, I had originally experienced a ton of problems with linked folders in KDS, so early on I abandoned that direction in favor of one that worked more reliably.