When you install applications to XenApp you place the server into “install” mode (using change user /install) to start recording per user registry key changes to the shadow key (HKLMSoftwareMicrosoftWindows NTCurrentVersionTerminal ServerInstallSoftware).
Occasionally the software installation requires a reboot part way through before continuing the installation. However, when you reboot the server is placed back into execute mode and changes are no longer recorded. But, you can’t place the server back into install mode before the installation continues.
What to do ?
One way the server knows how to continue the software installation after a reboot is to write the string to the RunOnce key at HKLMSOFTWAREMicrosoftWindowsCurrentVersionRunOnce. So, you can simply delete the appropriate part of this key, reboot the server, place it back into install mode and then manually run the command that was originally written to this key.
In this way you can still capture the changes made.
Other keys to check (just in case the installer utilises these keys) are: