I'm very new at this so forgive me if what I am about to say sounds stupid.
From my few days of messing around I have noticed when you target an npc and do #spawnfix and #repop zone it will move the npc to where you want it and it will update the X, Y, Z coordinates in the database.
Could you perhaps use this method to accomplish what you are trying to do instead of /loc since you think /loc may be giving you bad data?
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