If the student is in receipt of top-up funding and does have an EHCP you will need to update the SEN provisions to reflect the EHCP. To do this go to the support tab of the student's profile and click the cog next to SEN.
In this area click add new to record the SEN provision for EHCP. Please be aware if they are changing SEN provision you will need to enter an end date for the previous SEN provisions before adding a new SEN provision.
Alternatively if the student should not be recorded as in receipt of top up funding this can be amended under the support information heading of the extended tab on the student's profile.
As this is just a query if this is correct for your school when you upload the Census on Collect you can annotate the reason for this.