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@dscottf
You are right. There should be nothing wrong with your setup.
Maybe the metadata.db and/or metadata_db_prefs_backup.json are "broken" in some way or there might be something wrong with cops or apache?
What I do when testing cops is: (adapted for your situation)
1 - install cops in /var/www/html/ebooks (or whatever you want to call this directory)
2 - makedir /var/www/html/ebooks/calibre_ebooks
3 - only copy the database files for testing
cp /media/pi/MEDIA/calibre_ebooks/metadata.db /var/www/html/ebooks/calibre_ebooks/metadata.db and
cp /media/pi/MEDIA/calibre_ebooks/metadata_db_prefs_backup.json /var/www/html/ebooks/calibre_ebooks/metadata_db_prefs_backup.json
4 - edit config_local.php
$config['calibre_directory'] = './calibre_ebooks//';
In a browser goto cops (ebooks).
If there is an error then if possible try with other database files (just make a library in Calibre with no more than a few books).
Only on a Synology I had to "fiddle" with "open_basedir". Never on my Raspberry Pi. It should "just work". Ok, maybe change some permissions.
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