SID issues across large forest

I'm in the process of creating external one-way trusts to a master domain across several hundred different servers each with their own unique domain.

I've run into a massive problem, however, when deploying the configuration automatically a number of older servers are unable to join 'because file already exists'.  Upon further research, it seems my predecessor did not SYSPREP these domain controllers when converting them from a template and therefore can not join the domain without the unique SID.  (These servers are all VMs)

My question is, does anyone have experience with obtaining new SIDs for a production server that won't cause the domain controller(s) or SQL to burst into flames or am I SOL?

Thanks,
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Uptime Legal SystemsAsked:
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David Johnson, CD, MVPOwnerCommented:
dcpromo them to be regular servers
sysprep /generalize /reboot those machines.
activate the machines
dcpromo them back to be dc's

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zalazarCommented:
Please note that you have to be careful with generalizing a production server.
This as eventlogs are cleared, all unique system information is removed and system restore points are deleted. You might run into trouble with drivers but as it are VM's this will probably not be the case. Still try to make sure that all necessary drivers are on the local hard disk.
You could also look into adding extra options by using a xml file with sysprep and set options like PersistAllDeviceInstalls and DoNotCleanUpNonPresentDevices to true.
So not all plug and play devices are uninstalled/removed during generalizing.
https://technet.microsoft.com/en-us/library/ff716298.aspx
https://technet.microsoft.com/en-us/library/ff715820.aspx
Uptime Legal SystemsAuthor Commented:
Thanks for the comments, looks like it's going to be a painful process to correct these servers (a hundred or so domains) but I'll take this advice into consideration. Appreciate the responses.
zalazarCommented:
Thanks too and the best of luck.
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