It sounds like what’s happening is that your Mac’s storage is almost full, so it is offloading (evicting in iCloud parlance) some of the files to the cloud. Then when EagleFiler tries to read the file, it isn’t there (although Finder shows a placeholder for it). If you update to EagleFiler 1.9.4 (in public beta), that version will detect these evicted files and download them as needed instead of reporting them missing. Or, if you can free up enough space or turn off Optimize Mac Storage, you can prevent the files from being evicted in the first place.