Why is there a difference between the GSTR-3B summary in the GST Filing module and the GSTR 3B summary report in the Reports module?

The GSTR 3B summary report in the Reports module is just based on the transactions that have been added in Zoho Books. Whereas, the GSTR 3B in the GST Filing module summary includes the modifications that were made in the GST portal after filing.

So, if there is a difference between the GSTR 3B report and the GSTR 3B summary in the GST Filing module, it’s because of the changes that were done in the GST Portal after filing your return.