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You're not very specific about what issues the users are having in connecting to the terminal server—for everyone reading, the more specific you can be the easier it is to diagnose the problem, thanks!—but I'm assuming that they can't log in. From your description you have taken down the license server but not yet reinstated it fully with the license packs installed.
The licenses are transferable, but you can't do it yourself because the MS Clearinghouse ties those licenses to the license server you originally installed them on. Make sure the new license server is activated, then get your volume license agreement numbers or license pack codes. Then call the Microsoft Clearing House to get new CALs (client access licenses) issued to you. Once you've done that, you can install them on your new license server. You can find step-by-step instructions and phone numbers here at Microsoft's website.
As for particular issues with locating a Win2K3 license server, there aren't any that should be impacting you while the license server is located on a domain controller, so as long as the terminal server and license server are in the same site. A Windows Server 2003 license server can issue Windows 2000 TSCALs.
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