If I understand your question correctly, you're asking how the PCs saw the power, not how the players did? Basically, I decided each round which ability for each character would be shut off- and even for Epic PCs it tends to be a short list (if there's even more than one option). The character had no warning that the power wasn't there, in most cases, though the Bard who usually goes around incorporeal suddenly discovered to her horror that she couldn't just float right into the floor.
Basically, when the character tries to use the negated power, that's when he or she discovers it isn't working. For things that don't take actions to use, or are part of other actions, like the party tank's flying ability (which was negated early on in the battle, severely curtailing his movement options), this just forces the character to use other options (the tank just slogged on along the ground, such as it was- the battle was on a junk pile in the second layer of Acheron). If, on the other hand, the negated ability is a particular spell, such as when the party Sorceress tried to use Time Stop, the character tries to use it and it just fizzles- nothing happens. So that cost the Sorceress an action, but fortunately she has a few Greater Rods of Quicken so she got off another spell that round (I allow magic items to Quicken spontaneous spells- always figured it's silly to force casting time to increase if it's the magic item giving you the power to use it rather than the actual feat).
Some players may whine about unfairness, I suppose, but mine took it the way it was intended- as an extra challenge. It had the added benefit of making the players who had yet to act in the battle nervous, trying to think through and figure out which of their abilities were "shut off" that way. Extra layer of excitement, there. Plus, the players knew that if they won the artifact (which they eventually did), they'd have the chance to use this same power on enemies, and they were quite pleased about that. When the time came to use the Abrogate against enemies, I played it straight- the enemy had no way of knowing what was negated without trying to use it. And the enemy they used the artifact on indeed lost a couple of actions in the unpleasant discovery, to the players' delight.