How should I reconcile dot-underscore files after a manual backup?
dot_clean

dot_clean(1) Mac OS X Manual Page

Apple's description: 


  For each dir, dot_clean recursively merges all ._* files with their
  corresponding native files according to the rules specified with the
  given arguments.  By default, if there is an attribute on the native
  file that is also present in the ._ file, the most recent attribute
  will be used.
  
  If no operands are given, a usage message is output.  If more than one
  directory is given, directories are merged in the order in which they
  are specified.


Proceed with caution. Whilst the man page lists no known bugs, it is possible to lose data through careless use of the command.