In EP patent prosecution, aside from the requirements of novelty (Art. 54 EPC) and inventive step (Art. 56 EPC) that the invention must meet with regards prior art that has been published before the effective date of the patent application, the invention shall also meet the requirement of novelty with regards any EP patent (application) that was filed before the effective date and became public after the effective date or on the same date (Art. 54(3) EPC). This requirement forbids the double patenting of same subject-matter.
The Art. 54(3) EPC provision indirectly also considers PCT application designing the EPO as prior art that might be cited for novelty purposes as long as it was filed before the effective date and became public after the effective date or on the same date. Notwithstanding, for double patenting to exist in this scenario the PCT would have to be entered into the European regional phase. What this means in practice is that if there is such prior PCT application, the EP application that you are prosecuting cannot become a European patent until it is certain that the PCT application does not enter into the European regional phase. Therefore, the intention to grant communication shall only be issued by the EPO after:
- the 31 months for entering the PCT into the European regional phase have expired,
- the additional 2+ months for entering the PCT into the European regional phase requesting further processing (Art. 121 EPC) have also expired, and
- the PCT did not enter into the European regional phase by then
It is irrelevant that the prior EP patent application is refused or becomes abandoned and so no double patenting could exist, the novelty requirement will not be fulfilled in your EP patent application.
A minor difference between your subject-matter and the prior EP patent application will make your subject-matter novel. The prior EP patent application cannot be cited for lack of inventive step.