1) What happens if a machine is reloaded on the domain. Are we able to see the old information?
What exactly do you mean with "reloaded"?
2) Can we have alerts on if software is under license compliance. IE we have more installs than license.
Version 4 (beta) supports e-mail alerts
3) Does it scan users as they connect over our vpn tunnel? (Currently they vpn'in using the cisco vpn)
Version 4.0 (beta) supports the lsclient /scanonip switch for this or scheduled ip range scanning.