I found that balooshow -x <file> exists. When I run this for files that are shown in Elisa I get the line Property Terms: Maudio Mflac T2 whereas the files that aren’t showing in Elisa have the line Property Terms: Mapplication Moctet Mstream.
I’ll try purging and re-indexing to see if that fixes the issue (wanted to keep this as a last resort in case it takes ages to scan everything)