The CTRs are without error because now there is no SSN to match against the name.
That does not bless him as legitimate.
He told you that his SSN "was no longer good".
Which probably means he had a work permit for a fixed period and he has overstayed his time.
I assume the passport is valid?
So at the very least you may have an NRA working illegally in the country.
There are many of those.
I am not sure how I feel about yours though, as generally when I think of illegal workers they are earning minimum wage in the fields; yours has amounts over $10,000.00.
So back to the SAR, if you do not think fraud was committed then there is no need to file, but since you were concerned enough to have this conversation I would document the episode with a SAR Not Filed write-up and explained what has transpired.
If you forget about the fraud issue, you may want to file a SAR based on the dollar amount being cashed out by an NRA for work - if you think it is suspicious, and include his comments about his papers being taken from him.
Hope that helps you...