When you remove a Pokémon from the daycare, the data is not removed. It's simply marked 'Empty' and is only overwritten when you deposit another Pokémon into that slot.
PKHeX denotes this flag with ✓/✘ and fades out the preview sprite [relevant code here]. It's similar to Trash Bytes; the game doesn't care to clear unused data (saves some cpu operations).
Example 'Empty'
Example 'Full'
I prefer to not have the contents of the tab editable, as it may cause odd behavior ingame (ie, egg available for unbreedable species).