The position of the reference is outside the cell record it is attached to - listed as a child of the cell record.
This causes issue with the reference loading or unloading at the wrong distances depending on the cell being attached or detached.
If a reference was moved to cell 0,0 use xEdit to double check if the intention was to rather "delete" it. A properly "deleted" reference should have the Initially Disables flag set, the XESP - Enable Parent set to opposite the player character and its z position set to -30.000 but its x,y position should not be changed just like the typically undeleting operation of xEdit does.
How To Fix Intentionally Moved References
Open the mentioned plugin in xEdit.
Unfold the plugin in the left tree view. Right click [+] Worldspaces. Select Apply Script...
Select the script Put worldspace references in the right cells and click OK to execute it.
The messages log should list the references being moved.
Close xEdit and save the plugin.
If there are issues in the area, with references or their LOD themselves, consider generating a new LOD patch from scratch.