Every time i play menagerie all my unlocks are reset and taken away. In the top right of my screen a new chalice appears, and my other is replaced. This is really annoying and i can't be constantly grinding runes just to play one menagerie run.
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After each Menagerie run, it gives you a new Chalice because it uses the runes. Your purchased upgrades at the bottom should still remain purchased; it doesn't reset those. So, if you're talking about how it uses the Runes; that's intended. The Runes are supposed to be eaten when the Chalice is used to open the Chest.
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Do you have a video clip of this by chance?