the field called File Reference on a Payment File Administration auto generates the payment file we upload to the bank. This file has a reference to the company name which has since changed. Anybody knows how this file is generated and where we can configure the settings?

I'd look in the template for that payment file format and see where it gets the value from. Payments > Setup > Payment File Format. Bank File Template

Thanks for the pointer - had a look at couple of the templates that I thought might be the ones that generate the file, but haven't seen any references to the company name

Where is the reference located in the file?

the reference is pointing to the company bank details record - which is showing the old company name references, so I think here it is...

Seems right 🙂