Did anyone else not receive the last item?  Is it cause I had already graduated or? 

Hi, I was not graduated and did not receive the [Event] Fughar's Special Season Gift Box

I also had all of my pen Tuvala gear stripped! 

Correct, if you already graduated, you don't get the season box.  That mail is a bit misleading.

I had checked the mail and received all 4 items, but I kept them in my inventory without opening them. Now I graduated my season character and the blue box is gone. I don't know what was in it and I feel cheated out of it. Since when do items get removed out of my inventory?

The character the box was on was not the season character.

Oh, just realized the 3k stones were deleted as well. Yeah guess it's on me for not selling them right away. Imo shouldn't even have been given in the first place if they just get deleted. But whatever.

Yeah, they changed when season items get deleted.  Used to be "end of season", but now that that doesn't apply, it's "when you graduate". I suspect more people will run into this little surprise.  It's documented, but is buried in the notes.

It IS misleading, not just a bit. 

It doesn't cover "everyone" and it should say exactly that . I would have been fine with:

- [Event] Fughar's Special Season Gift Box (You will not receive this item if you have already graduated, This item will disappear from you inventory once you graduate.)

I'm sure it's ot that hard to add a few lines to the mail. Alas.

same happened to me, even didnt make 2nd ring and earring cuz i counted them from the box in...