If the original files each have one page and a limited number of the pages need corrections, you can create corrected input files that each have one page per file. When the pages are refined, the original incorrect pages are overwritten. Page assignments are preserved.
This approach makes page revisions indistinguishable from pages without revisions in the final job.
Example
The original job files are book.page1.pdf
through book.page98.pdf.
Refining the job in Prinergy creates the files book.page1.p1.pdf
through book.page98.p1.pdf.
The corrected files are called book.page2.pdf
and book.page74.pdf.
Refining them in Prinergy creates the files book.page2.p1.pdf
and book.page74.p1.pdf.
This overwrites the existing refined pages and keeps any existing page assignments.