I frequently have models that are organized in/by what I call a Master Site model/file. This file is the Parent in the shared coordinate relationship for all the children/siblings models/buildings that I link into it.
When model positions are changed in this parent file I find it is sometimes (often) necessary to use Publish Coordinates on all the linked models, even those that have not been altered. I've observed inconsistent results where sometimes the location of a linked sibling does not adjust (update) when viewed (as a link) within another sibling model. Using Publish Coordinates seems to force these linked files to refresh properly when a model is opened, even though it might seem unnecessary for those that didn't change.
As such, it is possible that seeing other linked files appearing to be out of alignment for this reason may motivate us to try to reset everything. Pause, breathe...try using Publish Coordinates on all the links first.