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

Solution 1:

You can copy the files using Finder. It seems Finder can reconcile these when copying from a partition type that doesn't support extended metadata to a partition type that does, reversing it's procedure for doing the reverse and creating the dotfiles.

Solution 2:

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.