It will depend heavily on a couple things, but we'll try to help you get it sorted out.
1. What process is being used for the upgrade?
2. Are the client systems managed by a PGP Universal Server?
If you are simply backing data up while the system is on, then installing a fresh Windows 7, then migrating the data back to the system (e.g. Windows Easy Transfer), you would not need to decrypt. You could simply reformat the drive, then install the new OS, and migrate the data back. You would want to be sure the user's keyrings are part of the data that is being backed up (they are in My Documents/PGP) if they use anything other than PGP Whole Disk Encryption.
If you are using an in-place upgrade, you would need to decrypt. I'm not sure why those recovery disks wouldn't work for you if they are the correct version, but I would avoid using the iso/recovery disk to decrypt a large number of systems. It is the slowest way to decrypt. If you are looking for something more akin to a script that you can push to the clients to kick off decryption, we don't officially support the scripting, but I can give you an example that you could modify to suit your needs.
In a managed PGP environment, where there is a WDE Disk Administrator Passphrase for the encrypted clients, you could alter the following script to fit your environment, then save it as a batch script to run on client systems to begin decryption. This would allow you to start decryption remotely by pushing the script via GPO or third-party distribution methods.
1. The following script is NOT officially supported, but merely an example of a script that should start decryption when saved as a batch file and executed on a client system.
2. The following should work on 32- or 64-bit clients.
3. Substitute your WDE Disk Administrator passphrase where it says AdminPassphrase.
@echo off
if exist "C:\program files\pgp corporation\pgp desktop\pgpwde.exe" (goto 32-bit) else goto 64-bit
:32-bit
cd "C:\program files\pgp corporation\pgp desktop"
goto decrypt
:64-bit
cd "C:\program files (x86)\pgp corporation\pgp desktop"
goto decrypt
:decrypt
pgpwde --decrypt --disk 0 --passphrase AdminPassphrase