In general, if a woman forgot to perform a bedikah on the onah beinonit, she should do so as soon as she remembers, even if some time has passed. If relations took place in the interim, an appropriate type of teshuva would be giving tzedaka. In addition, steps should be taken to prevent recurrence – reviewing the halachot of vesatot, putting reminders for veset dates into her phone, etc.
However, if a woman consistently has cycles longer than 31 days, there is halachic dispute whether she would be required to observe the yom hachodesh or onah beinonit. We follow the position that if she has at least three consecutive cycles longer than 31 days, she would only observe her yom haflagah, and not the yom hachodesh or onah beinonit. Should she experience a cycle less than 31 days, she would observe all of the onot until she reverts to her longer cycles.
Therefore, depending on the specific details of her past three cycles, your wife may not have been required to observe the onah beinonit and does not need to do a bedikah until her haflagah.
Please feel free to get back to us with any further questions.