This case modifies the imported prefab data but does not save it back to source file. So the imported data has become out of sync with the source data since the change was not saved back to the .prefab file. In Prefab Mode we open the .prefab source file that is why the values does not match the modified imported prefab.
Since 18.3 prefabs are imported which means that changing state on a imported Prefab Asset needs to be saved back to the .prefab source file if this changes should be persisted and reflected in existing prefab instances.

Below is an example of how you can save a change back to the prefab source file after changing the imported Prefab Asset:

Modified from ItemLibrary.cs from the repro project:

[ContextMenu("Save")]
public void Save() {
for (int i = 0; i < items.Length; i++) {
if (items[i] != null) {
GameObject itemPrefab = AssetDatabase.LoadAssetAtPath(AssetDatabase.GetAssetPath(items[i]), typeof(GameObject)) as GameObject;
Undo.RecordObject(itemPrefab.GetComponent<ItemObject>(), "Updating Item " + i + " Component");
itemPrefab.GetComponent<ItemObject>().item.ID = i;
PrefabUtility.SavePrefabAsset(itemPrefab); <-- ensures saving change back to the .prefab file.
}
}
}