...But the EMH could replicate new brain stem nerves for Ptera in "Emanations", restoring her back to life.
Also, the technique used for repairing Worf's spine in "Ethics" sounded suspiciously like replication, even though the name "genetronic replicator" may in fact be misleading.
There obviously are degrees to what can be done, not strict categories. New brain stems are okay, even with the resources of a damaged and stranded starship, but new lungs for Neelix are not. A culinary obsessive might insist on 100% lifelike steaks and get what he wants, but at high cost; somebody else would accept the same taste and texture as achieved by different means, through replicating something that's only 20% like real steak but features suitable "cheats" to enhance/"restore" the taste and texture to match natural.