Here is a small clip (about 10%) of a drawing, after replacing the assembly with a newer version of the same assembly. The only difference is one feature, which was added to the original assembly then "Save As" for a new file name, appending "REV B" to the end of the filename.
As you can see, all of the references are broken. Is there any way to repair this without redrawing everything?
Try doing a Pack and Go of the original Drawing, renaming the new model as part of the process, then make the changes to the new model. The references should stick that way (unless, of course, your edits remove some references).