First of all, b'sha'ah tovah.
According to most opinions, you continue to keep the onot perishah for the first 90 days after you last went to mikveh before conception. Thus, assuming you do not have an established veset (veset kavua), you would keep the same date of the Hebrew month as the beginning of your last period, the onah that comes out at the end of the same interval as there was between your last two periods, and the thirtieth day since your last period.
Practically speaking, once you have missed your first period, you will have no date from which to calculate the interval, the Hebrew date, or the thirtieth day. Therefore, if you do not bleed, then you will keep these onot perishah only once. If you do experience bleeding, then if you are within the 90 days you calculate onot as described above. If the bleeding was within the 90 days but the new onot you calculated come out after the 90 days, then you do not have to observe onot perishah. If you have bleeding after the 90 days have passed, you observe the date of the Hebrew month and the interval date, but not the thirtieth day.
Rav Moshe Feinstein ruled that, following a positive pregnancy test, a woman conducts herself as if 90 days have already passed. Thus, she calculates onot perishah only if she bleeds during her pregnancy. You may want to consult with your Rabbi as to which position to follow.
Please note that bleeding during pregnancy will make you a niddah. Staining during pregnancy is subject to the usual rules of stains; onot are generally not calculated from stains. You should, of course, consult with your physician about any bleeding during pregnancy.
This internet service does not preclude, override or replace the psak of any rabbinical authority. It is the responsibility of the questioner to inform us of any previous consultation or ruling. As even slight variation in circumstances may have Halachic consequences, views expressed concerning one case may not be applied to other, seemingly similar cases. All health and health-related information contained within Nishmat's Women's Health & Halacha Web site is intended to be general in nature and should not be used as a substitute for consulting with your health care professional. The advice is intended to offer a basis for individuals to discuss their medical condition with their health care provider but not individual advice. Although every effort is made to ensure that the material within Nishmat's Women's Health & Halacha Web site is accurate and timely, it is provided for the convenience of the Web site user but should not be considered official. Advice for actual medical practice should be obtained from a licensed health care professional.
For further questions or comments:
The Nishmat Women's Health and Halacha Site is a public service of Nishmat, The Jeanie Schottenstein Center for Advanced Torah Study for Women. This project and others like it are made possible by contributions from people like you. If you have benefited from the service, and wish to enable us to help others, click here to donate.
Users of Internet filtering services: This site discusses sensitive subjects that some services filter without visual indication. A page that appears 100% complete might actually be missing critical Jewish-law or medical information. To ensure that you view the pages accurately, ask the filtering service to whitelist all pages under yoatzot.org.