The domainValue_1 will happen if a Domain with same name already exists in the Enterprise gdb.
Are you Copy\Pasting all the data together, or one by one?
If you do all the data together, then the chances of these Domain_Value_1 is less.
Alternatively, you can try exporting all the content of the File gdb as an XML file (Export to XML Workspace document) and then import the XML workspace doc into the Enterprise gdb.