"When I ran the script it eliminated all of the records with empty quantity fields, but it also removed all of the sub parts from the report, so I just had a list of records without any of the banded categories I had set up."
In Browse mode, you cannot delete a part. What happens is, if you do not sort by the leading part (the break field) then the that grouping and its summaries (or any fields you have placed in the part, will disappear.
So if you create a report with two leading parts - MonthYear and then Category, you MUST sort by MonthYear and then by Category. :-)