I agree this needs to clarified legally not only for EN 60601-1 but also for the many other harmonized standards manufacturers have to deal with.
In defence of German Notified Bodies, there is 2004 document
ZLG 3.5 A1, (in German) issued by the their competent authority which instructs them to issue non-conformities and withdraw certificates if technical documents are not updated to current harmonized standards prior to the date of withdrawal. So this may be coming from a higher level.
The main point that I am making is that retrospective application is impossible, if applied broadly.
A classic example: in 2001 a brand new standard appeared (IEC 60601-2-37:2001) which had major new tests for acoustic output and transducer temperature for diagnostic ultrasounds. At that time, few manufacturers had the equipment to test, even the larger companies had older sets up based on FDA requirements, which are different to IEC tests. Establishing a test set up takes around US$100,000 and 3-4 months. It takes around 1 weeks to test a single transducer; many manufacturer have 100's of transducers. Taking into account testing, (re)design time, transfer to production and the supply chain, a reasonable transition period for such a major standard would be at least 3 years, if not 5 years.
The actual time line for this standard was:
2001, July: First published as IEC
2002, June: First published as EN (by BSI)
2002, Dec: Harmonized without any transition period
In other words, just 17 months from IEC to harmonization, and 6 months from EN to harmonization.
It is almost for sure that zero (0) manufacturers complied with EN 60601-2-37:2002 on 13 of December, 2002, and it is also likely that zero (0) notified bodies were checking to make sure implementation was in place before the deadline.
A strict interpretation would require all diagnostic ultrasounds to be withdrawn from the market on 13 December 2002, placing the European public at serious risk, as well as failing to comply with the top level EU treaty on laws.
This is not an isolated case, there are many like this, including recent examples.
Thus, we are left with two possibilities:
1) the NB interpretation is wrong, or
2) the law is impossible to comply with, potentially dangerous and illegal
Out of these two choices, the first seems to be most likely.