I would not be so sure that it is your former customer that is writing the checks. We have had checks come in with our routing number and an incorrect account number several times - some with actual customer or former customer information some with completely unrelated information. In our cases the checks were printed up by traveling check cashing rings and/or in connection with card cracking rings.
If you don't know that it's your customer that's writing the checks and you have no knowledge of who actually is - once the SAR threshold of $25,000 for no known conductor is reached, you should file. If you know or strongly suspect your customer is involved, use the standard $5,000 threshold and report it.
In our case, the report led to a capture and conviction of an individual who was a career criminal who had been traveling through small towns bilking mom and pop stores that cashed checks out of tens of thousands of dollars.
Knowledge is knowing what to say. Wisdom is knowing when to say it.