I would have Dr review the guidelines for repair. OpNote sounds like an Intermediate to me as dr doesn't explain any subfascial work or EXTENSIVE undermining. Most of the time the dr will have to undermine in order to close. If dr truly did a complex repair, they need to describe in CPT verbiage how they did it in the OpNote. An auditor isn't going to allow the DR to code for something just because they said they did it. They will want an explanation of how it was done.
Regardless of that, you can not justify modifier -59 (for CMS) on the repair as separate and distinct because it's a direct result of the excision. If you want to fight it you can try to copy the Guidelines you were referring to before, send a copy and highlight that CPT says to report Complex Repair Separately. Just be sure that DR documents extremely well and you might have a shot however long it might be. CPT Assistant April 2010 supports the reporting as well.
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