Consequences of non-payment of additional fee(s)
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The lack of an ISR and WO-ISA in respect of those parts of the international application for which no additional search fee was paid does not, of itself, have any influence on the validity of the international application. However, the national law of any designated Office may provide that the non-searched parts are considered withdrawn unless a special fee is paid. For further information see the national chapter for the designated Office concerned in the WIPO PCT Guide. 
WIPO PCT Guide 7.021 
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If the EPO is ISA, non-payment of an additional search fee has the following important consequences in the further procedures before the EPO: 
the EPO as IPEA will not perform the international preliminary examination in respect of any claims relating to an invention for which no additional search fee was paid and, therefore, for which no ISR was established (see point 392393)
upon entry into the European phase the EPO as designated Office will consider whether the application, which in the meantime may have been amended by the applicant, meets the requirement of unity of invention. If not, the examining division will invite the applicant to pay, within a period of two months, one or more further search fees in respect of any unsearched inventions claimed upon entry into the European phase in order for these to be covered by a further search (see points 654655 ff).

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