You can remove line items from a quote in both the Web Portal and the App.
In the Web Portal go to Accounts > Quotes > edit pen for the quote > select the red box with the x in it on the right end of the line item > Save and Close the quote.
In the App go to Accounts > Quotes > select the quote > Edit at the bottom of the page > select the red box with the x at the end of the line item >scroll down and Save.