That is very annoying, to say the least.
First of al, make sure that Correct Face Attributes is un-checked (might mess things up and is an easy step):
But my (wild) guess is, that it is your Data Transfer Modifier that is messing things up.
Try deleting it together with your duplicated Mesh, fix your Unwrap duplicate the half of your Mesh again and add re-add the Modifier.
If this doesn’t help and @jlampel also has no idea, maybe post a link to your .blend file (via Googledrive or Dropbox or something like that), so that we can have a look (there are many good troubleshooters in this community!)