Should I re-engineer my FSD under the new system?

The short answer is: Yes.

The longer answer is: Yes, but if you're concerned, upgrading a separate FSD and comparing performance will lay that concern to rest.
 
My AspX has a VERY good FSD under the old engineering system (56 lys). In the beta, I re-engineered it and gained nearly 3 lys. Once I'm back in the bubble, I'll re-engineer it for real.
 
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