RESOLUTION
Starting from Virtuozzo 4.0 it is possible to make pv2 migration from physical server running Windows 2000.In general the algorithm of migration is the following(the steps Virtuozzo does):
1. Copy and install VzAgent and Acronis snapshot driver to source server.
2. Restart source server.
3. Get and validate source server OS information and IP configuration.
4. Make source server partition snapshot(s) and transfer it (them) to Hardware Node. (Compose 8.3 file names as Acronis does not store them.)
5. Create Virtuozzo loopback(s) (virtual disk drives) and copy files from snapshot(s) to loopback(s).
6. Create initial VE configuration.
7. Upgrade VE.
a. Remove Windows 2000 system files and registry keys.
b. Create links to Windows 2003 OS template.
c. Convert IIS 5.0 metabase and ISAPI filters to IIS 6.0.
8. Set VE IP configuration.
P2V migration from Windows 2000 does not guarantee that all installed applications will work (fully or partially) after migration. Even Microsoft gives no assurance of this for its upgrade procedure from Windows 2000 to Windows 2003. However there are known applications that require some preparation before upgrading to higher OS version.
The most striking example of such preparation is adprep utility. This Microsoft tool extends Active Directory schema so that Windows 2000 Domain Controller becomes fully operational after upgrade to Windows 2003. Unfortunately we cannot automate execution of adprep because it requires Windows 2003 installation files.
So if the source Windows 2000 node is Domain Controller, one should launch adprep before P2V migration. Here is the detailed instruction on how to do this.
Actually Active Directory is not the only one application that requires additional efforts but it is the most commonly used so it was tested thoroughly (as far as it possible).