I am running a freshly downloaded vanilla Alfred 4.3 with Big Sur version 11.1 on an iMac. After upgrading to Big Sur (clean install), Alfred was not able to find folders/files in a folder named, "Calibre Library" which was located in the top level home folder and contains many thousands of files (epub, pdf, & jpg). Spotlight is able to find all folders/files in the Calibre Library folder. Alfred finds all other folders/files except for those in the Calibre Library folder. I re-indexed Spotlight using Alfred Rebuild macOS Metadata with no change in results. I moved the Calibre Library folder into the Documents folder thinking there may be an issue searching in the top level home folder; still Alfred did not find any folders/files in the Calibre Library folder (and re-indexed Spotlight). I added the Calibre Library folder to the Search Scope in Alfred; still no results. I ran Alfred File Search Troubleshooting routine and all tests passed; I tried several different folders/files in the Calibre Library folder as well as the Calibre Library folder itself -- all passed.
After creating a new Calibre Library folder and moving all the folders/files into the new folder (deleting the old empty folder), Alfred was able to find all folders/files in the new Calibre Library folder -- success! However, after shutting down the iMac and restarting, Alfred is no longer able to find any folders/files in the Calibre Folder even after re-indexing again.
Any suggestions on how to proceed? Could there be a permissions issue that I cannot see with the Calibre Library folder/files?
I forgot to add that access was granted to Alfred in System Settings (Accessibility, Full Disk Access, & Files and Folders).