I've had omegas on Grievous and Magnaguard for quite a while now. Will I get those omegas back for the ones that are replaced by zetas during reworks or will I get the zeta abilities upfront? That would really stink if they don't grant zetas and I just lose those omega mats
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Magnaguard will most likely get a new ability that has a Zeta option, the same way they did with B2.
The other abilities will probably also be improved staying level 8 omega abilities.
It depends on the ability. His basic and two specials aren't likely to get zetas, they'll probably have their effects changed--but whatever level you have them at now, you'll get that automatically when the change goes through.
His unique and leader ability don't currently have omega level effects, so most likely they'll get changed and have the zeta level added on top of that.
So you won't lose anything with this rework.
HOWEVER. I had all my bounty hunters with omegas when they got reworked and given zetas and wound up losing the omegas So even though you're not losing anything with Greivous (probably) that doesn't mean you will never lose anything going forward.