Are you saying that ISIS is not finding the dark and flat files you entered in the general page when you run the data reduction?
I have developed my way of working with ISIS over several years so I probably don’t do things the standard way. I collect all the files ISIS needs to do a data reduction in one folder titled with the target name and date, copying the masters, instrument response and wavelength calibration files etc in from other folders if necessary, rather than have ISIS search for them in different folders. (See attached example from a run last night) That way, although there is some duplication of files, I can archive the folder and always rerun the reduction again using the same set of files in the future. When I run the reduction I point ISIS to that folder in the settings page and point to the individual files in that folder the general page.