Start fresh when progression matters
A fresh save is best when you want the full 1.0 pacing: early base choices, technology unlocks, Pal captures, breeding setup, and late-game systems arriving in order. It makes new mechanics easier to understand because each upgrade appears as part of a normal route instead of being dropped onto an old base that already has habits and clutter.
Keep the old save for late-game testing
An older save is useful when the goal is to inspect new Pals, compare breeding routes, test World Tree systems, or stress a production base without rebuilding everything. Treat it as a test environment: verify what still works, note which routes changed, and rebuild only the systems that are actually blocking progress.
Hybrid approach for returning players
The safest choice is often to keep the old save and also start a small fresh run. Use the old save for quick checks and the fresh save for learning the updated progression. Once the new systems make sense, decide whether the old base is worth reorganizing or whether the clean save has become the main world.