I do it this way:
1. make paragraph styles in your certificate file before you run your data merge
2. make a TOC that reads those style
3. have the TOC float outside the art board in the first page, update it before making the .pdf
4. run data merge
5. Make a .pdf for print and include bookmarks
6. from acrobat open the 350 page .pdf
7. From acrobat go to organize pages and split, before you run the split go to the output option and choose to save separate files and named them using the bookmark names.
Hope this helps. I do this every year for a client, run 2500 certificates. For us the certificate number is a serial number, so they want the certificates to be saved all individually plus for the file name to be the serial numbers in the certificate from the data merge.
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