Yes affidavit seems good, but I will suggest making the affidavit when the applications will be near as there is still more than 1 month for the release of online applications for pmsss.
Till then you can talk to the tehsildar office about the procedure of changing the pin code i.e correction of domicile certificate.
During the verification center if the invigilator points out the mistake you can show him the affidavit officially signed by the concerned authorities and can tell him that you have given the application for the correction of the domicile certificate.
The difference is not so big but still do these things to be on the safer side at the time of verification of documents for pmsss.
Don't worry everything will be fine.