I've done something similar to this with Citrix. If I found the old version present in the registry then I needed to uninstall any old version, reboot, then run the install for the newest version. There is probably a better way, but what I ended up doing was this:
1. uninstall old version if exists in registry
2. use the 'Download from Source' delivery method to place the install files for the newest version of app on the local hard drive. (you could just use batch to copy to the local drive)
3. create a Service to run as SYSTEM, configure to run Automatically, so that it starts when the computer is started, and doesn't require a user to logon.
4. the Service will start a batch file that will use CMD /C for another batch file (which was copied to hard drive in step #2) that will kickoff the install.
5. use 'CMD /C Shutdown.exe -f -r -t 300 -c "Rebooting in 5 minutes after Install". This will run the Shutdown/Reboot after 5 minutes, allowing you to finalize the cleanup, and run an Inventory Scan.
6. run Full Inventory Scan - "C:\Program Files\LANDesk\LDClient\LDISCN32.EXE" /NTT=core_server:5007 /S=core_server /I=HTTP://core_server/ldlogon/ldappl3.ldz /V - hopefully it will complete within the 5 minute reboot window.
7. part of the cleanup would also be to delete the service that you created. SC STOP ServiceName, then SC DELETE ServiceName
8. exit program using EXIT /B returncode - where returncode is any code you want to pass it. I usually just pass 0 (zero) that way Landesk sees it as Successful. You could pass other codes depending on how the other steps complete, and then setup the Distribution task to accept these codes as failures, and successes.
Hope this helps.