I tend to agree with both Jim and Marc here. The essential problem is a breakdown in your own organization's Contract Review. The fact the customer supplied conflicting prints (paper and CAD) should have been recognized BEFORE you began manufacture.
If I were the arbiter trying to sort out whether the customer owed you money for the SNAFU, I might have chided the customer for its laxness in configuration management, but I would assign 100% of the cost to your company.
ERGO: root cause is simple - your organization, when faced with instructions (the drawings) in two different media (paper and electronic), had a duty to compare the two for anomalies. Good practice would have dictated prior agreement with customer on how the manufactured item would be inspected, which most likely would have included a controlling document. Did your inspectors inspect while viewing the CAD file on a computer screen or did they work from a printout? IF from a printout, whatever happened to the original paper drawing supplied by the customer? Were CAD file and paper drawing dated or versioned? Was one more recent than the other? Were there any obvious alterations to the paper copy (redlining in aerospace) which might have been a clue to its being the more recent version?
In terms of making NICE NICE with the customer, you can hope for a negotiated delay to avoid nonconformance on delivery date, BUT be sure to nail down inspection criteria (characteristics, attributes, AND class of instruments used for each feature) BEFORE you start again. I would confess the discrepancy was not noted - remain quiet after that - the customer may "offer" to subsidize the extra cost out of guilt for its own laxness, but don't hold your breath.