Off the top of my head, it sounds like your files are Xreffed in "relative path"... That is something you only get one opportunity to define while initially XReffing it into your file.
When you get to the screen where it asks you to define placement, and all that, in the upper right area, it defaults to Relative path. Which means if the file you're referencing is two folders back, it will remember that.
You move that file to another location, the file you're referencing is no longer "2 folders back" and now can't be found.
So you have to repoint the file location.
It'll prompt you and ask you if you wish to make the same changes to other Xrefs because it's assuming you're referencing all the files from the same folder.
If you wish to not use "Relative Path", the only fix is to detach, Xref again, and toggle "Relative Path" to "Full Path"....
Ideally, Relative Path is preferred though, but there are instances where Full Path is needed.