Generally, for Thermo methods, you want to export them on the instrument control PC. This is because they use a multi-stream writer to write their methods which requires all of the component software to be present to write the entire method. That means you would need to create a fully comparable environment on your personal computer, including chromatography software, etc. in order to be able to merge a transition list with your template method from your instrument PC.
So, for Thermo especially, you really want to copy your Skyline document to the instrument PC (usually using File > Share to created a .sky.zip file or upload to Panorama and then download). Then open the file in Skyline running on the instrument PC and do the File > Export > Method there.
That said, we are currently having issues with exporting to Altis methods even once you get past this error message. I think I have a workaround ready to go out this week if you are running the 3.0 version of the software, but not the 3.1 version. I am working with Thermo on this issue.
I would still recommend you get past this error message and familiarize yourself with the required steps to export a method without errors, but currently on the Altis this will likely just give you a copy of your template without the transitions from the Skyline document, because of what we believe is a bug in the Thermo library we use.
Thanks for posting this issue to the Skyline support board.