Could you send us your files so that we can try to reproduce this problem?
You could send us your Skyline document, and the template file that you are providing to the "Export Method" dialog.
It would probably also be helpful if you could send us the method that you exported from the new Skyline which does not work as well as the method that you exported from an older Skyline which does work.

In Skyline you can use the menu item:
File > Share
to create a .sky.zip file containing your Skyline document.

Files which are less than 50MB can be attached to this support request. If that .sky.zip and/or your template method file, or either of your exported methods are larger than that, you can upload them here:
https://skyline.ms/files.url

What exactly do you mean "invalid in MassHunter version 10.1"? Are you seeing some sort of error message?
-- Nick