A revised Loan Estimate was issued December 2nd (interest rate was locked on the 2nd and the APR increased over .125%). The tracking for the LE shows the borrower viewed it on December 5th.
Initial CD was issued December 5th (same APR as the revised Loan Estimate) and the tracking shows the borrower viewed the CD, also on December 5th. The loan closed on Dec. 9th.
The final LE was not received 4 standard business days prior to closing. The initial CD with the increased APR was received 3 business days PTC and issued within 3 days of the lock date.
Since the CD was issued with the correct APR 3 business days PTC and within 3 days of the Change of Circumstance (lock date) does that negate the LE issue?

I say no, as it is based on receipt date. If the revised LE was not delivered until: the 5th based on the mail rule, then your CD should not have been issued until the 6th.

The consumer must receive any revised version of the disclosures required under paragraph (e)(1)(i) of this section not later than four business days prior to consummation. If the revised version of the disclosures required under paragraph (e)(1)(i) of this section is not provided to the consumer in person, the consumer is considered to have received such version three business days after the creditor delivers or places such version in the mail.

Okay, thank you!

The issue is that the LE was not received 4 business days prior to closing. Not that the CD was issued improperly. The TRID requirement is that the LE can not be issued on or after the date the CD has been provided and revised LEs must be received at least four business days prior to closing. There is no specific requirement that the LE must be received prior to the issuance of the CD.
 
§ 1026.19(e)(4)(ii) Relationship between revised Loan Estimates and Closing Disclosures. The creditor shall not provide a revised version of the disclosures required under paragraph (e)(1)(i) of this section on or after the date on which the creditor provides the disclosures required under paragraph (f)(1)(i) of this section. The consumer must receive any revised version of the disclosures required under paragraph (e)(1)(i) of this section not later than four business days prior to consummation. If the revised version of the disclosures required under paragraph (e)(1)(i) of this section is not provided to the consumer in person, the consumer is considered to have received such version three business days after the creditor delivers or places such version in the mail.

Same difference. If the LE was not received until the 5th, you cannot issue the CD on the 5th just three business days before closing. Either way it is a violation.