A family of Microsoft spreadsheet software with tools for analyzing, charting, and communicating data.
Just do what you said - copy the workbook that contains the hyperlinks from main folder (1) to main folder (2).
DON'T USE FILE > SAVE AS FROM WITHIN EXCEL TO CREATE THE COPY.
Hyperlinks to files in or below the folder containing the workbook which contains the hyperlinks are normally created as relative links and so they will automatically reference the files in and below main folder (2) when you open the copy in that folder.