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I would bring up the issue of two passports from the same country when you visit the GE office because the only time you should have two passports on your TTP account is if they came from different countries. Even though the replacement is the valid one, the audit picked up two different issue and expiration dates and probably canceled your participation based on this anomaly, I would hone on his possibility as a reason for being dropped from the program and be prepared to explain this. Bring both old and replacement passport.

Ask them if the GE office can send a message describing the anomaly and what was done to reinstate your participation in this program.They are likely to listen to an CBP officer who performed the corrections than to rely on the user.