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Also, after this partial rotation, you're supposed to wait for all buffs to cooldown, and then restart it again right? As in, don't start up Internal Release even though Blood for Blood is still on cooldown just to maximize dps?
No. Never hold your buffs to try and sync them unless you only need to hold them like ... a few seconds. Only hold buffs for fight-centric mechanics (Titan Heart, Twintania Conflag or Snake debuff). Do not hold buffs "just to sync". Synchronizing them is good, but not worth holding the buffs for any meaningful stretch of time.
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Lastly, what exactly is clipping? In my interpretation, it's for example, Chaos Thrust is at 4 seconds left and then you hit the IDC combo so Chaos thrust is refreshed even though CT is already at 4 seconds? How does this lower dps?
Because you didn't need to refresh the CT so soon. You've "wasted" 4 seconds of the CT debuff due to unnecessary overlap.