GL-PCT C IV 3 Late-filed reply after a first or further WO-IPEA (408) has been sent

In the PCT procedure, there is no loss of right for applicants if they do not meet the time limits for replying to a written opinion. The only risk the applicant takes with a late reply is that it might not be taken into account for establishing the IPER.[Rule 66.4bis; Rule 80.5; Rule 82; Rule 82quater; GL/ISPE 19.32; GL/ISPE 19.50; ]
 
In practice, if the applicant's reply is received after the time limit set in the WO-IPEA (Form 408) but before an IPER (Form 409) has been started, the late-filed reply is taken into consideration for drawing up the IPER.[GL/ISPE 19.33; ]
If a reply is received after the IPER has actually been started and the applicant has not met all the objections set out in the last written opinion, the late reply is not considered and the IPER is drawn up on the basis of the conclusions set out in the last WO-IPEA.
If a reply is received after the IPER has actually been started and all the objections set out in the last WO-IPEA have been met, the late-filed reply is taken into consideration for drawing up the IPER.
If no reply has been received, the IPER is drawn up on the basis of the conclusions set out in the last WO-IPEA.

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EPO PCT GL - C Procedureal Aspects Chapter II

PCT Implementing Rules