I did a quick test using Laserfiche Server version 10 and Laserfiche administration console version 10.
RepostioryA in ServerA contains windows acct1 and acct2, export into an xml file, then go to RepositoryB in ServerB which already contains acct1 (all in one single domain and same Active Directory Server), then through Laserfiche Administration console I choose to Import Repository Objects, browse to the xml file and select option "Create new objects only if matching objects do not exist" .
Under windows account section in RepositoryB it display the acc2 , acc1 as I mentioned before already exist.
What version of Laserfiche server are you using?
what option do you select from drop down list "Conflict Resolution Import Options"?
What is the size of the xml file?
How many accounts are included in the xml file ?
As quick test, you can try to export only one windows account in an xml file, then confirm if importing a single windows account works or not.