The only other example I know of is the situation in Cyprus. On accession to the EU in 2003, the northern part of the island was, and remains, de facto controlled by Northern Cyprus; a state created after the 1974 invasion by Turkey.
As a consequence, in the treaty which set out the state's accession, the EU laid out how the issue would be handled.
In particular, Article 1 suspends the application of the 'acquis' - and therefore, the EU's de facto territory - in areas of Cyprus not effectively controlled by the government, while reserving the right of the Council to withdraw this suspension, presumably on reunification.
The application of the acquis shall be suspended in those areas of the Republic of Cyprus in which the Government of the Republic of
Cyprus does not exercise effective control.
The Council, acting unanimously on the basis of a proposal from the Commission, shall decide on the withdrawal of the suspension referred
to in paragraph 1.
Article 4 is also relevant; it allows the European Council, acting unanimously, to alter primary law - the Act of Accession 2003 - in order to provide a simplified procedure to accommodate a reunification or territorial change. A primary law change would usually have to be ratified by all member states.
In the event of a settlement, the Council, acting unanimously on the
basis of a proposal from the Commission, shall decide on the
adaptations to the terms concerning the accession of Cyprus to the
European Union with regard to the Turkish Cypriot Community.
This 'pre-ratification', is as far as I'm aware, the closest example to the Northern Ireland & East Germany situations.