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The good news is that you won't need to re-build anything. That said, I see 2 ways to update your file.
- Save the original as a template (before it's merged) and run the merge again once the CSV has been finalised. That way you always have the template of the first and each time you run the merge you get a new indd file.
- The other is based on the assumption that you added your merge fields into the document and not the master of the original file. If so, you can copy the document page content into the master pages, add the merge fields to the master and use this as a template. When you merge the document this time the CSV becomes a linked file in the resultant file.
The differences between 1 and 2 is that the link to the CSV file is kept in the merged file in 2. Either way, it's a very easy update for you but you will have to re-apply your custom changes. This should just involve a straight copy/paste though.
Yes, we have been leaning toward a similar option as your #1 at this point. However, #2 is what we prefer. I moved everything to master pages (2 page spread). Then, I can run data merge and it works fine. Then, if I update the CSV file, open InDesign and then choose "update content in data fields" it will display the changes i made in the CSV file...only issue is, it then converts our 2 page spreads into single pages within the pages pallette. When you attempt to put them back as spreads, it messes up content, etc. I can send you an example if you direct message me.
Actually, all it is doing after we "update content in data" is only applying the left page of the master page throughout and that is why there is single pages after the update. I can send files to anyone that may explain the issue