IMHO, you should send the AFT notice out to the affected customers and get the signed authorizations back. Document your efforts from the identification of the problem to resolution.
You should probably include a "we need this back by" date in your cover letter to the clients, as well as a follow-up campaign from the account officers to get the forms in since most people will not open the letter and read it.
For those who do not return the form, I would turn off the auto-debit feature since you don't have a contractual agreement that authorizes you to draft the account under AFT. Of course because of the precidence you have set by your practice, there could theoretically be Reg E change in terms notification due for that (maybe include that in the cover letter and make the drop dead date 21 days out from the date of the letter?).
You might want to look further than just training. If it is an overdraft LOC only that cannot be accessed by any other means than a sweep to the DDA, consider hard-coding your system to always check the yes box for that loan type if you have a separate loan type for just that product.
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I can't herd the cats anymore, so I just set up the electric fences and let them fry when they stray out of bounds.