I would like to hear how others do this as well.
The way I do it is that all my existing lines have their status set to existing and I add the suffix "(E)" to the end of the line number.
For example, I create a line number in the format SERVICE-NUMBER. Size and Spec will get added automatically, to create final tag in format SIZE-SERVICE-NUMBER-SPEC.
All existing lines would follow like: GP-1234(E)
The new parts of that existing line would be: GP-1234
Then I run iso's on only the new lines and I get continuations symbols to the existing lines.
The ISO BOM is supposed to exclude items marked as existing. I don't know why it's not for you.
When creating an overall BOM, using report creator, the existing pipng (status is existing in properties) is still being called out in the overall BOM.