@haydeningham If the values in the DB are being serialized as integers then there is a 99% chance this is being done by something other than ACF. A filter, or possibly calling update_field() with an array value containing integer ID values rather than strings.
I have run into this in the past when building my bidirectional relationship plugin. When getting getting values of the field using get_post_meta() I need to convert all values in the array to integers before working and then convert them all back to strings before updating. Since you mention bidirectional fields it’s possible that this is the cause of your problem.
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