GL B VIII 4.2.2 Reply filed in time

If applicants reply to the invitation under Rule 62a(1), indicating an independent claim in a particular category which they wish the EPO to search, the EPO will conduct the search based on this claim.
In reply to this invitation, the applicant may also indicate more than one independent claim in the same category for search, where these fall within the exceptions provided for in Rule 43(2) (see F‑IV, 3.2). However, if the applicant does so, but the EPO finds that the claims indicated do not fall within the exceptions provided for in Rule 43(2), only the independent claim with the lowest number indicated by the applicant will be searched.
Example 
If an application contains independent product claims 1, 10 and 15, an invitation under Rule 62a(1) is sent and the applicant contends in the reply that independent product claims 10 and 15 fall within the exceptions provided for in Rule 43(2) and indicates that these two claims are to be searched, but the search division does not agree, then only claim 10 will be searched.
Where the applicant attempts to file amendments, the procedure indicated in B‑VIII, 3.2.2, is followed.
In any timely response to the invitation under Rule 62a(1), applicants may, instead of indicating the independent claim or claims to be searched, simply argue why they believe that the claims comply with Rule 43(2) (i.e. why the plurality of independent claims in the same category fall within one or more of the exceptions provided for in Rule 43(2)). If the search division is convinced by the applicant's argumentation, a search report will be issued on the basis of all the claims, and the consequences of a limitation of the search which apply in examination will not ensue. If the search division is not convinced, it will issue a search report for which the search will be conducted based on the first independent claim in that category. The final responsibility as to whether an invitation under Rule 62a was appropriate lies with the examining division.
Furthermore, the applicant may, in reply to an invitation under Rule 62a, file arguments against the findings in the invitation requesting as a main request that the claims as filed be completely searched and as an auxiliary request, in case the search division is not convinced, indicate the independent claims to be searched (see also H‑III, 3.2).
The applicant may phone the search division in order to enquire about the course of action after an invitation under Rule 62a has been sent, as explained above for the invitation under Rule 63 (see B‑VIII, 3.2.2).

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EPC Implementing Rules

EPO Guidelines - B Search

EPO Guidelines - C Procedureal Aspects of Substantive Examination

EPO Guidelines - F The European Patent Application

EPO Guidelines - H Amendments and Corrections