The issue seems to be caused by the save been overwritten as the game can't be saved while another level is loading and the trigger to begin loading the next level is located very close to this particular flower.
I was able to replicate this twice but every time I've tried since then it has worked normally. All I can suggest is that you try waiting around in the room for ~30 seconds before using the WAU flower. If the game successfully saves, you should see the save icon in the bottom right corner of the screen.
Mav__
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HPL Modding for SOMA and Amnesia: Rebirth. Current available mods by me include: SOMA: Mavs Hard Mode SOMA: Cutting Room Floor REBIRTH: No Crosshair Mod