Joshmo,
It is good practise to not screw up.
It sounds like you are on a non-intelligent CAD system. If you change item numbers on your parts list, you are going to have to search every single page of your drawing for every single instance of your items, and change each one correctly. What are your changes of getting this right, and what values is there in changing item numbers anyway?
Don't do it.
The next question is informational. You state in your revision block that you deleted the item as per the ECN. You can delete the line. You can remove the data from the line, leaving only the item number. You can cross out the data in the line, leaving it readable, but obviously (enough?) that it is not to be ordered or kitted. What do people need to know?
SolidWorks has the ability to cross out no-longer used item in the BOM. I choose not to use this feature because the cross-out is a Microsoft Excel format that may not transfer to a plain text database. You need to consider the limitations of your software.
JHG