I had this same exact issue a while back and found it was actually how the custom field keys were being saved in the database. Essentially, once you reach a certain character limit (length) inside the database for these keys, they stop saving. I brought this up to ACF support and was directed to purchase the ACF PRO version as they save these fields in a different fashion and with greater lengths. After upgrading to ACF pro, the issues stopped happening and now have very complex nested repeaters that work flawlessly. Also to note, you will not lose any custom fields or data you have created in the regular version as ACF PRO imports all of the old info. Hope this helps.
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