I notice that in cases where it is the left eye that is lost, it relates to a transfer of power, while losses of the right eye don't.
Examples:
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Fai's left eye is removed and eaten so that soullessclone!Syaoran can take his magical power. Real!Syaoran cannot use his left eye, since from that eye he copied his heart into clone!Syaoran's right eye. When Kokuyo gives his left eye to Hisui, he is giving her/him half of his power. Fuuma gives Subaru Seishirou's left eye, which gives Subaru the power of the Sakurazukamori.
Losing a right eye (Subaru, TB/X!Seishirou, TRC!Seishirou, clone!Syaoran, Doumeki, Watanuki, Yasha) doesn't cause a transfer of power. TRC!Seishirou and clone!Syaoran both have things "installed" in their eyes, though (the copied heart, the magical device to travel between worlds).
I'm not sure if there's anything to this pattern, but I find it interesting.