I found out that when creating a DataAsset from AssetTools, The load flag (bHasBeenFullyLoaded) of the created Asset is not set, It seems to be in a state where overwriting saving has not been completed due to that check.
Cmd: OBJ SAVEPACKAGE PACKAGE="/Game/SaveDataAsset/MeshLocationDataAsset" FILE="C:/Users/redacted.username/Downloads/328742-savedataasset/Content/SaveDataAsset/MeshLocationDataAsset.uasset" SILENT=true
LogSlate: Window 'Message' being destroyed
EditorErrors: New page: Save Output
EditorErrors: Warning: Asset 'C:/Users/redacted.username/Downloads/328742-savedataasset/Content/SaveDataAsset/MeshLocationDataAsset.uasset' cannot be saved as it has only been partially loaded
LogSlate: Window 'Packages Failed To Save' being destroyed
There's no existing public thread on this issue, so head over to Questions & Answers just mention UE-66435 in the post.