I would first thing go to the engineer and ask for an EVA.

Acquiring an engineering variance on a few deep indents may be a lot less effort and risk than a repair if the part can be judged fit for purpose.

Sometimes just because a thing is out of tolerance does not demand something really should be done.

You might be extra persuasive if you have a corrective action plan in your pocket to give the engineer confidence it won't happen again.

Just an idea.

Also  D17 is pretty strictly a welding specification, so other fabrication tasks like riveting, drilling, bends, etc., and the tolerances that go with them are likely to be found in the OEM standard practice manuals rather than a welding specification.