When applying the update set which contains the update about choices, choices from other languages won't be touched if there is no such language choice in the update set payload
It is by design that choices from other languages will not be touched if there is no such language choice in the update set payload, otherwise, it might cause the choices from other languages being removed over upgrade
Create an update set to capture the deletion of the choices as the following screenshot.
All other English choices were removed and two of them as recorded in the update set left. However all choices in other languages still exist.
There are only en language choices that are recorded in the payload. Therefore when the update set is applied, choices from the other languages are not touched.
Regarding deletion operation, mark the inactive field of all the choices that should be deleted to true, and make sure the update set captures the changes and then apply it on the target instance. Essentially, in the update set, keep at least one choice for each language, if you do not want the choice to be displayed on UI, just mark that choice as inactive=true, in order for the change on that language to be applied when the update set is committed.
Regarding other operations, make sure to update at least one choice from each language