It affects your actual stats. It is a very old bug that has been around possibly forever, but went mostly unnoticed prior to the Age of Sorcery as buffs that increased health or stamina directly were very rare before the attribute overhaul.

When you consume an item that gives you such a buff, you gain said buff. Then when you drink water or eat food up to max, you gain the full thirst or full hunger bonus which will overwrite the buff. Then, when the buff wears off naturally, the buff is subtracted from your health/stamina, causing it to go negative.

Until (if) this bug is ever fixed, I strongly recommend avoiding any potions or foods that provide bonus health or stamina.

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