Roodt Mentrual Cup Cleaner
It is sutable for both silicone and TPE cups and is made from natural ingredients. The power is effective in removing stains, odour and dried residue without leaving any particles behind. 
You need dissolve 1 spoon of this powder in very hot water and leave the mensrual cup in it for an hour. Since the powder is free from synthetic fragrances, you need not worry about any allergies.