The mystery says after flipping the relic, discard it to put an eldritch token on the mystery. However, the card isn't clear about the timing of this process. Do you discard the relic before following the instructions on the back of the relic card, or after? If after, some relics' instructions tell you to discard the card, so are you then unable to discard it in order to advance the mystery?

Does “Item – Magical Relic” count as a Relic? The mystery requires a relic to be flipped, and it looks like Magical Relics have different rules for flipping than a plain "Item -- Relic".

Question 1: See the second question in the FAQ section of the SR rules, but yes, you can advance the mystery by using a relic you discard as part of the flip effect.

Question 2: Yes, a magical relic counts as a relic. I can't find where this question came up before, and I'm not sure if it was here on or BGG, but I remember there was an official ruling that stated the magical relics count both as magical and as relics.

I can confirm with regards to Q2 that Magical relics do indeed count as a "Relic" for card puropses.

I received an official clarification from Nikki Valens who also mentioned that the traits format has changed with the release of Strange Remnants and would be noted in the next FAQ.

There was confusion because there was no comma between Magical and Relic leading some (Myself included) to believe that a "Magical Relic" was a different classification of item to one that just had a "Relic" trait.