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The Scenario

I am the DM for a group who have just entered a town that was attacked by cloud giants a few days before their arrival. The players and characters don't know this though, so part of the mystery is trying to work out what happened.
One of the characters is a Ranger with giants as their Favored Enemy, which means

Favoured Enemy - You have advantage on Wisdom (Surival) checks to track your favored enemies, as well as on Intelligence checks to recall information about them.

As an example, one of the major clues is the fact there are dozens of boulders scattered around the town that were dropped from a cloud giant castle from a great height. As well as footprints that were left behind when they eventually descended from said castle.

The Problem

Although the Ranger has giants as their favored enemy, it isn't immediately apparent that giants are at fault here (the town has been abandoned so there is no one to ask about what happened). However if the player asks to take a look at the boulders or tracks left behind, I would have to ask them to roll the check with advantage. This will immediately tip the player off that their Favored Enemy ability is coming into play as for anything else, that check would be made as a straight roll.

Obviously if the player succeeds on the check, it won't be a problem as they would have learned giants were here. But a failure on the check would provide no in game knowledge for the character, but still float meta-game knowledge in the air for the players.

The Question

Before a Ranger knows what they're looking at, how do I allow a player to use their Favored Enemy ability without providing spoilers on a failed check?

You make the advantage roll in secret

In situations where I don't want players to know they have advantage/disadvantage for any reason I simply roll a d20 for them myself and work out the results. This usually works out just fine because the players do not know if I am simply rolling an opposed check, for example.

I also make it a habit to roll d20s behind the screen for no reason which also helps with the ruse.

This does require that you either know their modifier or keep an eye on what their d20 result was and calculate it from there.

There is, however, one issue I have found with this method: it messes with abilities that allow players to reroll before knowing the results and things like the Lucky feat so it is not an universally applicable solution.

Roll a second dice behind your screen

If you want the ranger to unknowingly roll with advnatage then this is the simplest solution.

When the ranger makes his check, roll a second d20 behind your screen, then take the higher of the two rolls (his roll and your roll on his behalf) and give him information based on that, not necesserily the roll he rolled.

Your players will know something is going on when you roll a check but they won't know exactly what. If this is likely to be problematic at your table then roll a few d20's in advance of the session to use for this purpose and keep a note of the outcomes.

This is precisely what the passive versions of skills are for

The recommendations for when to use passive checks are:

Such a check can represent the average result for a task done repeatedly, such as searching for secret doors over and over again, or can be used when the DM wants to secretly determine whether the characters succeed at something without rolling dice, such as noticing a hidden monster.

To calculate the passive check value use this formula:

10 + all modifiers that normally apply to the check

Then compare that value to the DC for the check.

There are modifiers for advantage (and disadvantage) as it interacts with their passive perception.

If the character has advantage on the check, add 5. For disadvantage, subtract 5. The game refers to a passive check total as a score.

When I DM I get the players to fill out a character tent with their ability scores, proficiencies and AC that I can then refer to if I need passive check info.

You tell them

"You see scattered boulders that seem to have come from nowhere and large imprints in the ground. Giants have been here!"

Favoured enemy to me is like passive perception, you don't need to ask about something to recognise it.

Once they have been told about the giants they still have to make the tracking check, so they only find out so much.

How about you say that he is allowed to roll as if it were advantage, but you will decide, without telling him, whether you take the second roll into account depending on whether his skill applies or not.

Ofcourse, this means that you will have to do this on other occasions as well, to avoid shifting the meta from the problem with advantage rolls on Favoured Enemy, to meta on this "trick".

(Disclaimer: I'm very noob at D&D so I have no idea if there's anything in the rulebook, or some common practice for this.)