There is a halachic debate about how to handle this situation. Possibilities include: not observing yom hachodesh, since there's no thirtieth of the month in the upcoming month; observing the twenty-ninth of the month, since the period began at the end of the month; and observing the first of the following month, since the period began on Rosh Chodesh.

We follow the view that you should observe the first day of the month this coming cycle (1 Sivan). Since the onah beinonit comes out on the twenty-ninth of Iyar, you will, in effect, satisfy all the positions. Should your period arrive on the first of the month, there would be a possibility of establishing a veset kavua for Rosh Chodesh.

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