Does SKSE work with special edition? Thing is, SKSE was created for the 32 bit Skyrim, and Skyrim Special Edition is 64 bit, meaning the current version of SKSE won’t work with the Special Edition.
It usually marked as an “Application” under the Type tag. Open the FNIS executable configurations in Mode Organizer and ensure that the Begin In path and the executables are pointing to precisely the identical folder.