Hi Nima,
The setting are stored in apm_parameter_values. You will have to join apm_parameters.
You will need something like this.
update apm_parameter_values set attr_value ='YOUR NEW SIZE' from apm_parameters ap where ap.parameter_id = apm_parameter_values.parameter_id and ap.package_key = 'file-storage' and ap.parameter_name = 'MaximumFileSize';
Please kindly test the update statement above, its not 100% sure. But more or less that is the idea.