Yes, you could transfer entire data using Backup and Restore functionality. Follow the steps below for the same:
a) Go to Tools -> Backup repository -> Specify a location for tar file.
b) Go to Tools -> Restore Backup -> Select the .tar file created in previous step.

Following should be considered before trying Backup and Restore of data:
a) This function should be used across the same version of GeneSpring.
b) .tar file should be created on a file system without a size limitation. Do not use a FAT32 file system if the app folder size is greater than 4 GB.

It is recommended to consult GeneSpring Support (informatics_support [at] agilent [dot] com) before OS upgrade.
 
Backup and Restore will solve this issue. However, since there is no original filesystem to go back after your OS is upgraded, we strongly recommend to also perform the following:
 
a) Export important individual projects.
b) Keep a copy of the following:
           i) "app" folder from GeneSpring installation directory.
           ii) All previous repository data folders, if any.