You'll have to elaborate on this:
..won't let me insert new page numbers.
By what method(s) are you attempting it, and what happens when you do?
I deleted the master page with the footer that had the page numbers. I created a new master with a footer. When I try to go in and insert page numbers under Type-Insert Special Character, etc. all the options are grayed out.
When I go to Layout-Numbering & Section Options and try to start page numbering at a particular page the program tells me that a page setup already exists and that adding a new one will create confusion?!
When I try to go in and insert page numbers under Type-Insert Special Character, etc. all the options are grayed out.
You must set a text frame and have an active insertion point, (blinking cursor), when you issue the Type > Insert... command.
The Number and Section options are not tied to master pages. Just set it the way you want it. If an alert or error occurs, post the exact verbiage here to get help.
Your last response was blank....
The warning about duplicate page numbers is normal when you restart numbering with a new section. To remove the confusion you need to change the number STYLE in the dialog on one section. It's fairly traditional for front matter to be numbered using small roman numerals like i,ii,iii and and the body of the document to use 1,2,3.