Are your hyperlinks dynamic (created through the Identify tool) or field-based (listed in a field in the attribute table of your layers)? If they are field-based, you may find a solution with the Hyperlink Base.
The hyperlink base is accessed through File -> Document Properties. Enter the beginning of the path to your files, for example C:\GIS\GIS Database\ . All field-based hyperlinks in the document now use this as the start of the filepath to hyperlinked documents. The rest of the path - the part which changes for each hyperlink - is contained in the attribute table field.
So, if the targets of the hyperlinks are
C:\GIS\GIS Database\Folder 1\File1.pdf
C:\GIS\GIS Database\Folder 1\File2.pdf
C:\GIS\GIS Database\Folder 1\File3.doc
and C:\GIS\GIS Database\ is the hyperlink base for the document, the table might look like
ID, Field1, Field2, Documents
1, Value, Value, Folder 1\File1.pdf
2, Value, Value, Folder 1\File2.pdf
3, Value, Value, Folder 1\File3.doc
The hyperlink base shortens what needs to be in the table.
For the next step, instead of changing all the field entries to the new, shorter filepaths, could you make a list of them in Excel or something, add this as a new field in the table and call it, say, 'NewPath'? If you can then simply open the Properties dialogue box by right-clicking on the layer in the Table of Contents and open the Display tab. Make sure the Support Hyerlinks Using Field box is checked and the Documents option is selected (not URL or macro), then in the drop-down menu select NewPath.
Hope this helps.