With the item purchased and consumed, handynotes is reporting that this item is still missing. See below:

Could you please check if you have bought this on an alt?

Yes, it looks like I have purchased it on one of my alts. I cannot obtain it on my main though because it's a once-per-account deal. How to make handynotes aware of this?

For now we don't have a solution. We are tracking these items with hidden quest ids but unfortunately they are only on the char you have redeemed this item "true" for the other chars they are "false".

As @Dathwada says, we do not have a good solution for this at this time, which is why we include the note on Ve'nari:

If we can find a way to query the status of Torghast upgrades that does not rely on these quest ids, we can fix this later.