ACF stores the custom fields for terms in the options table. It will still be there, but the option_name will be wrong.
Lets say that you have the same term name my_term both categories and tags and that the id of this term is 10.
Lets say you have a custom field named ‘image’ attached to the category term.
ACF would store this value with the option name category_10_image that is {$taxonomy}_{$term_id}_{$field_name}
Now lets say that WP splits the term and when that happens the term_id of the term in tags stays the same ‘10 but the term id of the term in categories changes to 20.
The image is still stored with the same option_name category_10_image, but the ID value is wrong and the option name should be category_20_image. The field does not appear because ACF is looking for the second one but that one does not exist. With the way acf stores the field key there would also be a value with the options name of _category_10_image that should be _category_20_image
At least, this is what the problem is if this has something to do with term splitting. The only way to know this would be to set up a site on WP 4.1 or before that has terms in multiple taxonomies, set up some custom fields, look at what the term_id values are before updating and then update and look at the ids after.
I know this isn’t helping you solve your problem, and I can’t be sure if this is the problem.
