Thanks for the detailed feedback!

I was able to reproduce your issue: Ökonomie doesn't work, while Oekonomie and ökonomie are working. This is an issue in Joplin, but a workaround in the script can be implemented easily. I. e. converting all tags to lower case.

Edit: I opened a github issue: Tags starting with upper case special characters are not imported properly · Issue #11179 · laurent22/joplin · GitHub

I guess there is a problem on both sides: The script creates some odd URI and the Joplin import is not robust enough to handle it. You could try to catch the related error at the developer console ("Help > Toggle Development Tools"). Maybe it shows the name of the affected note.

That's strange. I couldn't observe this in the test files. Could you provide a example export here or send it to my email (linked at the end of the script output)? The more data it contains, the better for debugging. I guess that's the only way to find out if it's a bug in the script.