@Charles.C our finished product is considered NRTE
As I understand you are seeking a response to yr customer's finding L.innocua in the finished product.
This logically may derive from (a) the raw material / added ingredients and/or (b) the Production environment.
Assuming there are no specific bactericidal process stages, finished product micro. characteristics will, minimally, typically, reflect the raw material.
Detailed knowledge will require implementing microbial monitoring for (a) and an env. monitoring program (EMPG) for (b).
Various examples of EMPGs are shown here (wet/dry processes often focus on Listeria/Salmonella respectively) -
Not sure if the above answers yr query, if not please revert.