I'm not sure if this is the right place to report bugs for the GOG Version but when I obtained the Shabby Doll and stored it in the chest, it didn't disappear from the chest after I cleared it's haunting with a holy candle.

It's not a huge issue, since you can prevent obtaining it anyway. This might have been caused by the new update since I didn't have this issue before when I restored the haunting with a mod.