Update: All runes, upgrade materials and compensation have been sent in BossMail to players who lost runes earned from the Portal Event.
Additionally, and stated elsewhere: all upgrade materials and gems have been returned to players who purchased an Unbreakable Heart rune from the shop late last week.
We are aware that runes were deleted that were not intended to be - namely, the Unbreakable Heart rune from the portal event.
The gems for the runes in the shop yesterday (ATK/ATK/DEF Unbreakable Heart) were compensated for, and you should have a BossMail already with the gems spent (+ additional) on those offers - the gold and evo essence will be granted in a separate BossMail.
We are working on a solution to grant players the Unbreakable Heart runes from the portal event that were lost as well (with the gold and essence) - Expect that on Monday, or Tuesday at the latest.
It is unfortunate, and we sincerely apologize and thank you for your patience.