Re-reading your message, I may not have understood all the detail. You mentioned about deleting lines of text in the master page text box, but one thing to add about the primary text flow frames on the master page is that they cannot already contain any text.
I guess with problems like these it can sometimes help to share an image of the page setup, because for example for your catalogue there may be a different approach to the one you’ve taken for positioning the catalogue entries. I’m guessing you’ve created a grid on the master page with each entry being a separate text frame? And this is what you override on the catalogue pages to position each entry? Is your catalogue entry text one text file, or one file for each entry, or is it in a spreadsheet, for example?
I’m not sure my first answer is much help, but I’m sure what you’re trying to achieve is not too difficult with a bit more context!
Thanks
Nick