Question:
Is there anything that sfeik sfeika does not apply to? tumah and taharah?
Answer:
There are numerous cases where sfek sfeika will not apply. To really know when it will or won’t you will have to learn Y:D 110.
The Rema Y:D 110-8 says that an item that will become permitted in the course of time will not be permitted with a sfek sfeika.
Also tuma in a private domain will apply even if there is a sfek sfeika, see mishnayos Taharos 6-4, Rambam Hil. Avos Hatuma 18-1.