I live in Scotland too. The letter that you got, if the same as mine and my friends' (Galloway and Glasgow) was sent one to each residential property with a description of the registrations that had been migrated to the IVR, with a request for anyone whose details were incorrect or missing to fix it using the new system. Most of this should have been cleaned up on the old system last year with the high voter turnout for the referendum. However at least two MSPs (incuding Cabinet Secretary Alex Neil) were lost in the process.
The Electoral Commission stuff is reserved to the UK Government, so slights to the SNP or Scottish Government are misplaced.