Couldn't find anything where this has been changed/removed on purpose, so I'm assuming it's a bug -
Using the Windows Installer version, running the latest patched version: 3.5.8478
MusicBee is no longer detecting PDF's within sub-folders directly below the music files like it did before; there is no PDF flag displayed in the Track Information panel.
"show PDF file indicator" is still enabled and if I move the PDF file to be in the same folder with the music files and Rescan, the flag appears.
An example of the folder structure I'm using (music files are in the first location):
D:\Media\Music\Hip-Hop & R&B\Albums\The Game\[2016] - Streets Of Compton
D:\Media\Music\Hip-Hop & R&B\Albums\The Game\[2016] - Streets Of Compton\Artwork\Digital Booklet - Streets of Compton.pdf
Thanks.