I know there is a bug with certain quest items where if you find them early, you can't complete the quest when you later get it.

Unfortunately Pangea's Flute is in the same chest as the Staff I need for a Winterhold quest, and I don't have the flute quest yet.

If I just leave the flute in the chest, without having picked it up, will I still be glitched? Does merely seeing it in the chest items list count as discovering it?

If not, and I just take the staff and leave the flute there, will the flute stay there safely until later on?

Thanks for any help/advice.

While I can't say for certain, my best guess would be that you're not flagged as having the item unless you actually pick it up into your inventory. Just make sure you keep a save from before opening the chest

Great - let's hope so!

I really didn't want to spoiler myself too much in this game, but it feels like glitch-preventative spoiling is necessary not to run into major quest bug issues. I hope some more things get fixed in the next patch.