Lets say you want to move everything from /mnt/mergerfs/tv to /mnt/mergerfs/media/tv
cd /var/lib/emby-server/data
sqlite3 library.db
UPDATE MediaItems
SET Path= replace(Path, '/mnt/mergerfs', '/mnt/mergerfs/media')
where Path like '%/mnt/mergerfs%';
UPDATE MediaStreams2
SET Path= replace(Path, '/mnt/mergerfs', '/mnt/mergerfs/media')
where Path like '%/mnt/mergerfs%';
UPDATE TypedBaseItems
SET Path= replace(Path, '/mnt/mergerfs', '/mnt/mergerfs/media')
where Path like '%/mnt/mergerfs%';
.save