I want to remove some and change other items that are part of the packages that can be bought by the player. Best way to do this so it doesn't cause problems?

Dont delete anything. Ever.
Drag it below the floor and 'initially disable' it. (check box)

Just do not do anything with the 'master' object that enables with the package. Its usually an Xmarker. And it also controls all the child objects that enable with it as the parent object.