I’m afraid I don’t understand your question, so please forgive me if I’m wrong.
If you use a file field type and
acf/save_post to modify the value to something else other than ID, ACF won’t recognize it as a file and the backend will show the field as empty.
If you need to upload the files but don’t want it to show up in the media library, maybe you can upload it manually by using a PHP code? This page should give you more idea about it: http://www.w3schools.com/php/php_file_upload.asp, http://php.net/manual/en/features.file-upload.php.
I hope this makes sense 🙂
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