Finder advanced search for empty folders not working

I have a big set of folders that each contain one excel file. I now need to replace each of those files with another excel file, so my plan was to delete all of the existing files (worked seamlessly with advanced search) and then use advanced search to show me the empty files as I keep adding the new excel files in each folder. But even though I cleared out each folder, the search still doesn't return them when looking for folders with 0 items. Just to test it, I created an empty folder, which turns up in the search results. I checked for hidden files using ls -a in terminal and since I have never opened most of these folders, they shouldn't contain a .DS_store file. Any ideas?

I'm running Mojave 10.14.2 on a mid-2014 MBP, and the folders were initially created on Windows using an R script.