You cannot use save terms and load terms when you put a taxonomy field in a repeater. If you do this all of the fields will have the value of the last field changed.
When you use save terms, ACF updates the post terms to the term selected. It does not remember previous times that it did this so any terms previously added will be removed. Since you are also using load terms, whatever terms are associated with the post is what will be loaded and not what is saved in the acf field.
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