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This problem will still exist in the new version. The reason is that as each field is save it updates all of the terms assigned in each field, and removes the ones not there. It’s the way that taxonomies and terms works when updating them in code. This is covered in https://codex.wordpress.org/Function_Reference/wp_set_post_terms because the $append argument to the function is set to false in ACF and in 99% of cases this is the way people would want this to work.
What you will need to do if you want it to work differently is create an acf/save_post filter https://www.advancedcustomfields.com/resources/acfsave_post/, use a priority of 20 so it runs after acf. In your filter you will need to get the values from the repeater field and update the terms again yourself.
This is an older topic, but I thought this information might help someone else looking for the same thing.
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