The problem is that it's two files. One that has all the old markings, notes etc. and one that has all the new ones. I can combine them, but then the Kindle won't recognize it as the file that markings and notes should go to, and thus creates a new one.
I've just checked, the file that the Kindle writes into is called "my clippings.txt", on the Kindle it's called "Mein clipboard" (language is set to german)
Also, not sure what I did last time, but now it works lol. Just copy and pasted via editor. If I remember correctly, last time I used calibre, so I guess I edited the calibre file and then transferred that to the Kindle.
Problem solved then :P
Thanks anyway