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Guide for applicants, Part 2: PCT procedure before the EPO (Euro-PCT Guide)

Supplementary search performed: EPO was not ISA
If after entry into the European phase a supplementary European search is to be performed (EPO was not ISA/SISA), it will be carried out only on the invention or group of inventions first mentioned in the claims (as possibly amended upon entry into the European phase), regardless of whether an ISR was drawn up in respect of that invention in the international phase and regardless of any earlier findings as to unity of invention in the international phase.
Although the EPO is in no way bound by the opinion of the ISA on the question whether the application meets the requirement of unity, the EPO will, given the fact that the practices of the ISAs are based on the same Guidelines (Chapter 10 of the ISPE Guidelines), in many cases share that opinion. Therefore, where the ISA/SISA considered the requirement of unity not to be met, the applicant is advised to amend the application in due time in such a way that the invention on which the applicant wishes the supplementary search and the examination to be based, is that first mentioned in the claims.  
If a supplementary European search report is to be drawn up, the invention that was the subject of the supplementary European search is the only invention that can be examined (see points 648-649). If the applicant wishes a different invention to be examined he will have to file a divisional application.