For me, this comes down to compliance and a legal opinion.
The certification you make when lodging the electronic counterpart says that the lodging mortgagee "holds a mortgage granted by the mortgagor on the same terms as this Registry Instrument or Document."
If the mortgage was reviewed for any reason, whether it be a compliance check or challenged by the mortgagor, would your electronic national mortgage be deemed as being 'on the same terms' as the signed jurisdictional mortgage form you hold?
When this happened for us, we erred on the side of caution and discharged the NMF version and registered a correct jurisdictional version.
*Please note: I am not a lawyer and this is not legal advice*