There is a (convoluted) way to save the wanted tagged sections to a new document. The approach requires that you have everything in your document conditionally tagged.
1. Make a copy of your existing document (use Save As). [Very important step]
2. Hide all of the tagged content that you want to keep in your document.
3. Select all of the (remaining) unwanted content by using ctrl+A (Select All in Flow) .
4. Apply a (new) condition tag to this content all in one go - you can tag this as "Not_wanted".
5. Show the previously hidden "wanted" content.
6. Hide the Not_wanted tagged content.
7. Delete the Not_wanted conditional tag.
FM will balk by reminding you that this tag has been applied to some currently hidden content and ask what you want to do with that content: make it unconditional or permanently delete it.
8. Select the Delete option.
You now have only the tagged content left.