why are you accepting the data as DWG ? never mind ...
Make a back up of the whole folder elsewhere and edit the back up folder like this
using copy attachments instead of nested then make the changes to the xrefs from inside the xrefs only not the parent file.. then copy the original parent file over the top of this working copy..
this should maintain the viewports and all the settings relating to the original acad dwg file and let you update the xref models thru microstation..ref manager once your satisfied that it worked recopy all the modified files over the top of the original first folder... But do not edit or alter your true original supplied data that should be in your as received data folder and never be touched... just in case you need it again and its a true record of what you received ...
Clear as mud right?