Any staining found after the pipelle exam may be attributed to trauma and does not invalidate the clean days. You may omit bedikot until the staining subsides but should make sure to perform one final bedikah on day 7. If you are still staining on day 7, as long you performed daily bedikot on days 1-3 of the clean days, you may delay your final bedikah until day 9 if necessary. In that case, your days 3 and 9 would become your new days 1 and 7. If you didn’t perform any bedikot beyond day 1, and you are unable to get an acceptable bedikah on day 7, unfortunately you would have to restart your 7 clean days.
Going forward, we recommend reviewing the laws of ketamim, since not all staining will render a woman niddah. As long as you do not experience an actual flow (comparable to a period), you may take precautions against becoming niddah from this staining by wearing colored underwear and waiting at least a few seconds (ideally 15 seconds) after urinating before wiping. See our page on stains for more details.
Please feel free to get back to us with any further questions.
B’hatzlacha!
This response has been updated to reflect the rulings of our current Rabbinic Supervisor, Rav Kenneth Auman, regarding waiting before wiping.