If you exceed 6000 Power Cores, you will no longer receive duplicate power cores until you are under the 6000 power core threshold.
Instead, you will receive Energon rather than Power Cores.
To start receiving Power Cores again, you must fuse your Power Cores until you are below the 6000 cap.
The only exception to this rule is duplicates rewarded from combiner bots. These will continue to reward Power Cores.