A woman is planning to fully convert to Judaism but she fears her cycle may fall out the same time she goes to Mikvah. If she does have her cycle then will it interfere with her conversion? What procedures should be done at this point?
A woman that is converting to Judaism will not have any issue if she has her cycle while she goes to the mikvah. The ritual impurity of nida does not affect the geirus process negatively in any way, and her preparations for the mikvah etc. will be the same as if she didn’t have her cycle. If she sees blood after immersing she will be rendered a nida, however that will not interfere with the actual conversion in any way. (As a side point, in a certain way, having a cycle at this point is advantageous. There is a rule a single woman that converts has to wait 3 months before getting married. This is because just in case she is pregnant, we will know when the child was conceived. If she has her cycle while converting, or right afterwards, it is established that she is not pregnant, and she wouldn’t have that waiting period.)
Another point; Even if she already had her cycle, she does not have to count seven clean days, because the period that she had before she immersed in the mikva will not make her ritually impure. Therefore she doesn’t have to count for the period that she had before she became Jewish.
Hisorirus Tesuva 4-95, Geirus Khilchoso 4-26, Hilchos Geirim 5-29.