Lets say you are in a building with Unhallow that effectively has a Protection from Good up.
You enter the area with a Protection from Evil up. Is your Protection from Evil repressed while inside the the Protection of Good circle since the Unhallow is a higher level spell?
Or are both the effects repressed?
The way we ruled it as if you walked into an area with Deeper Darkness with a Daylight spell cast on you; the areas that overlapped would be normal illumination without the two spells.
[Light] and [Darkness] spells are a special case in the rules, where an area of magical light/darkness can be canceled out by an area of magical darkness/light.
In general, if the spell does not specifically tell you to cancel another spell out, don't do so.
In specific, unhallow has no effect on protection from evil.