I am aware of inventory respawn flag cos it is a massive pain in ass for non-follow wardrobe mod and needs to be handled, programmatically for a small footprint, but looking very loosely at the ShadowmereRef, I found no papyrus scripts, so when a cell resets, it might be spawning at the default editor location, like all other npc, horses, that for one reason or another, do not have persistence , etc so we are going into terrority of the game engine here. But I did not do this and just thought of it now, is the REF marked has persistent? Dunno forgot to check it, but it might be that simple.. but where did you last leave it now.. maybe respawning at set default editor location is a good idea.