Yes, the problem is that if you try to copy an existing line and move the new line (in the CS, by right-clicking on the new entry and use MovetoQuest; I have never had any reason to investigate how to do this in TES4Edit), the original line will show up as edited, with a * in front of it. Cleaning this in TES4Edit is probably too much work to be worth it.
I think I would open two instances of the CS to be able to copy and paste as quickly as possible.
The real work, however, is to add the linking to other topics and to find and rename the voice-files. So, maybe it's still easier to use copy/movetoquest and then clean afterwards in TES4Edit. If you use this strategy, make sure that you move the NEW entry and not the original one!
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the original line will show up as edited, with a * in front of it. Cleaning this in TES4Edit is probably too much work to be worth it.
Not true at all. If you want to make an interior in every city that uses the same floor plan as the vanilla player home or someone else's home in Skyrim it is far faster to duplicate and get a dirty edit to clean later. Same with dialogue or anything else. If it takes more than 3 steps to do to get the basics it is worth it. cleaning in tes*edit takes one action, right click and remove. rebuilding from scratch takes far more steps for everything. You have a characters dialogue that uses the vanilla voice files if you duplicate the quest that has all the dialogue you just have the one quest to remove, takes as much time to remove as to set up the quest priority if built from scratch and maybe less. Once you have everything you want it is a matter of making it work for your NPC by changing only those parts that are NPC specific.
Take a female armor for Skyrim, duplicate the Armor and Armor Addon of a vanilla armor you want it to match in specs then all you have to do is swap the models in the AA and redirect the armor to the AA and it is done. rebuild from scratch and you have 10+ minutes in the AA alone compared to the same time used being fully finished.
Interiors though... every farmhouse kit inn in Skyrim is a copy of 1. Including the Granskog inn! They all have the same error and that's a wreath embedded in a wall. remaking the floorplan compared to cleaning is counterproductive and why I do not call Wolf out on the copypasta. He was smart to copy. 1 person spends 8 hours creating and perfecting then 100 others uses that after is a great use of time management. It is just smart to reuse what's already done.