Could be a good time to call your European Notified Body to see how they are going to handle changes to certificates for EN ISO 13485. Strangely, the transition period is over....it was zero (0) days apparently. The harmonisation of the older versions of both standards expired on the same day the new standard was harmonized - 30 August 2012.
The normative sections (requirements) in EN ISO 13485:2012 and EN ISO 14971:2012 do not differ from the pure ISO versions they are based upon (see below). Therefore, these updated versions will not impact conformance with those requirements.
EN ISO 13485:2012 Medical devices - Quality management systems - Requirements for regulatory purposes (ISO 13485:2003)
EN ISO 14971:2012 Medical devices - Application of risk management to medical devices (ISO 14971:2007, Corrected version 2007-10-01)
However, as pointed out in the updated informative Annexes, some aspects of the applicable European Directives (i.e., MDD Annex II, AIMDD Annex 2, IVDD Annex VI) are "Not covered" by any normative clauses of the standards. Hence, compliance with EN ISO 13485 requirements does not provide presumption of conformity with all the aspects of the applicable Directives.
Therefore, a manufacturer or a Notified Body may have to take additional actions to ensure conformity, and claim or certify conformance, with Annex II/2/VI of the Directives. The Directive requirements must be examined, applied and verified one by one and the solutions adopted must become part of the quality system.
What does this mean? (in my opinion)
Notified Bodies will need to examine how they have been auditing against the MDD Annex requirements to see if the updated informative Annexes might raise the bar with regard to their conformity assessment methods.
Manufacturers should review these updated Annexes to see if they should update their quality system procedures and/or deliverables (e.g., Risk Management Reports) to ensure coverage of the Directive requirements that are not addressed in 13485 or 14971.