Hello Jeff,
SDK Project Refresh will only pull in files from a newer SDK than the one they were created with. I tried to replicate this issue by adding a new folder to an SDK project and linking the folder to my project in the Includes and in Paths and Symbols.

However, after I refreshed SDK components my folder was still included into my project and the include directories remain the same. Please check my snippet below after refresh.

Maybe you can share steps to replicate your issue on my side? Also I did not face any compiling issues.
Best regards,
Felipe