My wife makes bread in small quantities that don’t require the separation of Challah. She stores these amounts in bags in the freezer. My question is, if many breads accumulate in the freezer if it remains like a "Kli" where the Halacha is that if all the breads even not baked together are put it one basket (of the Shiur Challah) the basket combines them and one has to separate Challah.

Yes, be careful never to put a Shiur that reach Challa together.