If we use a zeta to upgrade our anima will we lose it?

[Rath]

There's no solid answer yet, but I very much doubt that our old relics will be consumed in the process. The game keeps track of what quests we've completed so I think it's more likely that if it detects we've completed the the last relic quest chain it will enable us to take advantage of the shortcut in the anima quest chain.

First relic required us to get a base weapon, our zodiac will probably replace that base weapon.