We had this come up in one of our recent games and weren't quite sure how this would work out.
BBEG got revived in the middle of the encounter and has Champion features such as Blade Ally, which provide the effects of a weapon property rune to a specific weapon he wields. They are also a Graveknight, which also makes any weapon they wield function as a Frost weapon.
Both the Blade Ally feature and the Graveknight ability do not mention being magical in nature or having magical traits of any type, contrast to the Tyrant reaction they possess, which has literally every trait under the sun.
In the midst of the combat, an Anti-Magic Field went off through the entire room, turning all of our magical gear and effects into mundane stuff (i.e. they were suppressed), which is why this question was brought up.
The GM ruled that because the abilities were natural (Blade Ally attached to a spirit inhabiting the sword, Graveknight abilities are innate to any weapon they hold) and not magical in nature (no traits or direct linkage to being purely magical runes), the properties would apply to the weapon (in this case, Unholy and Frost).
We beat the encounter regardless, but are they right or wrong by RAW? Did we miss something in the rules that is glaringly obvious?
In your hands, the item gains the effect of a property rune
The Blade Ally itself might not be disabled by an anti-magic field, but all of the Property Runes that I am looking at all have the Magical trait - so they would be magical and would be disabled by anti-magic field. So if your PC's runes stopped working, so should the granted rune from the Champion's Blade Ally. Gaining the weapon critical specialization effect would still work.
But while I would have ruled differently, it is slightly ambiguous. So I can't fully fault the GM for ruling that way.
It's the simple fact that it gains the effect of the rune, and doesn't add the rune itself that gave pause to that initial decision, simply because a ghost, while supernatural, isn't dismissed from an Anti-Magic Field. It's also the reason why it stacks with other potential property runes on said weapon.
I would still have the Divine Ally adding all of the effects of the rune - including that it is a magical effect.