Actually, Preservation did destroy a part of himself permanently, or more accurately, Leras, his vessel did. Leras sacrificed the greater portion of his cognitive to imprison Ruin. Shards don't actually have their cognitive, they're just large pools of spiritual energy which require a host to provide cognitive. I agree though that Leras did separate a portion of Preservation's power entirely, the portion that became the Well of Ascension, essentially a closed system from the rest of Preservation. When Vin released the power of the WoA it rejoined the rest of Preservation, terminating the prison around Ruin's cognitive.
Also, while the power used to create the WoA was returned to Preservation afterwards, Harmony is still more Ruin than Preservation since Preservation still has a bit more of itself invested into humans than Ruin.