Package bundles are setup to prompt once per task, not once per package. However there are a couple things you could do. To stay closely aligned with your current method, you could modify your prompt and state that the device will reboot twice over the next half hour (for example). Although some users may not read the prompt that closely. You could also modify your script such that it pops up a window and notifies the user that an install is still in progress, and warns them of an impending reboot. Off the top of my head the scripting commands don't come to mind but I'm sure someone has worked this out on google. You may need to use a vbs or other script type.
Another option is to change up your deployment methodology considerably. Using the Office Customization Tool you can specify an option to remove old versions. Here is some info on that:
With this tool you can execute setup.exe /admin and step through the entire install while making configuration choices including whether to remove old versions. You will end up with a config file and you can deploy office in one package, instead of multiple packages in a bundle.
Another option is to use a provisioning template. You can separate your bundle into individual packages, and then configure multiple template actions, one for each package. The provisioning GUI will be on-screen the entire time, and will reappear after a reboot.
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Thanks for coming back to me! Funnily enough people not reading is exactly what management want to try and avoid so I like the idea of a in progress pop up box .. I shall look into that!
However, I hadn't thought about Provisioning templates at all so that is indeed worth some investigating.