You entered keys one at a time, then bought a pass. Now you have a screen full of rows and one pass row that covers all of them.
Nothing is broken. Here is what to do with them.
The short answer
Enter your pass, and the individual rows stop mattering. A VIP Access Pass enables updates for the whole library, so every item you added by hand is already covered by the one pass row.
You will notice the screen changes once a pass is on it. Before a pass, product rows come back on their own if you remove them, so the screen offers to clear the key instead. With a pass entered, the rows are genuinely removable and an X appears against each one.
Clearing them out is tidiness, not maintenance. Nothing breaks either way.
The case for keeping them
There is one situation where leaving them alone is the better call, and it is easy to miss.
You have a 365 day pass, and some of your individual purchases were lifetime.
Lifetime items keep getting updates forever. Your 365 day pass does not. If the pass lapses and you have already removed those lifetime rows, the items they covered stop updating along with everything else, and you have given up something you paid for.
Leave them in. They cost nothing to keep, and they carry on working the day the pass runs out.
If a row will not let you remove it
A row with a status of Active is locked. That means the store is holding a site activation against that key, and dropping the row here would strand it against your license limit with no way to claim it back from this site.
Click Deactivate on the row first. Then it unlocks and the remove button appears.
Adding the pass
On the Update Keys tab, use Have a VIP Access Pass? at the bottom of the screen rather than typing the row by hand. It knows the exact item names and it only offers you tiers above whatever is already on the site.
Passes work as a ladder. A site needs one, not several, so moving up to Lifetime retires a 365 day pass rather than sitting beside it. The picker tells you which ones it is about to retire before you commit.
A trial is not a full pass
If what you have is the VIP Access Pass (Trial), none of the above applies yet. A trial covers a subset of the library for a limited time, so it does not replace your individual rows and it will not displace a key you own. Keep everything exactly where it is.
The Update Manager itself
If you were buying individually, you were entering an update key for the Update Manager too, or you were supposed to be. A full pass covers it now, the same as everything else. See Does the Update Manager need its own update key?
Full procedure: How to enable auto updates. What a lapse changes: What happens when my pass expires?