Hey @Jacco 
just out of curiosity, are you trying to change any part of the option values for those particular variants or swap variant IDs between products?
For example, if you’re trying to rename a product option but keep the metaobjects the same, we’ll return this error. There’s a bit more info in this thread here, but in cases where you need to adjust product options directly, we recommend using something like productOptionUpdate (you can update multiple options with this mutation, including removing, adding, etc.).
Just wondering what your use case is here/if that’s what you’re doing - happy to help out further 