If all your customizations were done to wiki pages (and not directly to files
server-side), then importing the xar should create an identical instance on
B.
Maybe something went wrong during export ? Did you have error messages ?
Another thing that can be checked, is the content of the generated .xar :
it's a zip file format, and folders structure maps pages structure. This way
you could see if things are missing in the .xar (pay attention also to empty
files).

In you point 2) you say you imported then logged as admin, didn't you log as
admin before importing ? If not, you could retry this way, maybe you didn't
have sufficient rights during import to overwrite some existing pages if you
were not logged as admin user.

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