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You can probably just activate the key to add the additional content you are missing. No need to remove anything. That's the case with some other games anyway.

Hmm, not sure but if you have a base game with DLCs, you should try activating that key 1st as at times the latter key overwrites though there is a small chance there maybe an error.

I think if you remove the complimentary titles from SEGA, you are not able to restore them as they are not activated by you in the 1st place. Thus, truly removing them from your library permanently. I've not tried but I usually avoid doing so unless i really wanted to remove the game.
Cheers~

Perhaps contact Steam and explain the end goal? In my case, I got Renegade Ops in Sega's MWNL this year, but I was later able to activate a key for the complete pack from a Humble Bundle for the DLC even though it included the base game.