The list is the EU terrorist list. It is a list of people and organizations that are considered terrorist and that is compiled by the Council of the European Union. People and organizations in the list are subject to restrictive measures (like freeze of assets).
About the PKK, the article is rather clear. According to it:
A European Union court ruled against the way the Kurdistan Workers Party (PKK) was put on the bloc’s list of groups whose funds must be frozen to help fight terrorism in 2002,
The ruling does not say that the PKK is a terrorist organization, nor the opposite. It says that when in 2002 it was included, it was done without following the proper procedure (there were not enough reasons provided for the decision). So the inclusion of the PKK in the 2002 list was not valid.
But an EU official said a new version list had been drawn up in December 2007, including the PKK again, which took into account the views of the court in similar cases in the past.
That means that the answer by the EU Council is that in 2007 they did it right, so even if the inclusion of the PKK in the 2002 list has been invalidated, the inclusion of the PKK in the 2007 list remains in effect since -in the opinion of the EU Council- that time they did it in the proper way.
So, to take out the PKK from the list, at least the 2007 list (or the most recent one) should be challenged in court. Note also that in the page that I linked to there is a reference to Hamas and, according to that, if the PKK were to win such a lawsuit and the Council were to appeal that ruling, the PKK would remain in the list until the appeal was decided.