Tosafos explains that we cannot create a sfeik sfeika for a woman who gave miscarried over a 2 day period, to be metaher her on the 15th day of her miscarriage, maybe most of the child came out on day 1 so she will enter days of tahara on 15, and if it only came out on day 2 maybe it was a male so there are only 7 days of tu'mah. The reason we can't use this sfeik sfeika is because there is a contradictory sfeik sfeika that one will use on day 41 to be metaher the blood she sees on that day. Maybe she miscarried on day 2 so that 41 is still within the 40 days, and maybe it was a female so that she is still in yemei tahara.
From this Tosafos the Pri Megadim (y.d. 110 - additions to kuntres of shach 1) says that we cannot use a sfeik sfeika when there is another upcoming halacha for which we will want to use an opposite sfeik sfeika, since it is an inherrent contradiciton. However, it is not clear whether we disallow this type of sfeik sfeika since both sfeikos are in direct contradiction to one another. But, in a case where only one of the two sfeikos will be used in contradiction, maybe we can still rely on sfeik sfeika. The Pri Megadim proves from Tosafos in Nidah 27a that even if just one of the sfeikos contradict, we cannot use that safeik as part of a sfeik sfeika.