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In a case where the PCT national phase 30 month date has already passed, there is no way to enter this PCT application into the national phase in Japan.
If you would like to attempt to protect the invention described in the PCT application anyway, you may be able to file a new application directly with the Japanese Patent Office, adding new matter relative to the lapsed application. As long as the subject matter has a proper inventive step, all claims from the PCT application can be presented in the new application as either directly or indirectly dependent on a claim defining the additional subject matter. Of course, it is not possible to claim priority from the lapsed PCT application.
There is no way to disclaim the earliest priority date at the national office level (at the Japanese Patent Office). Also, it is no longer possible to withdraw a claim of priority in the international stage according to PCT Rule 90 bis. 3. Such a request should have been filed within 30 months from the earliest priority date.