Haven't tried it with 1000s of instances but there is a feature in the Visual Studio designer under the Process Instance Management tab.

You can retry a specific error and specify the version to retry it on.  You can also check the option to retry all error instances to auto-retry for all error instances with the same error.

Thanks Jonny. Since the issue is occuring in production we dont have Visual Studio Designer installed in the server. Is there any other way of doing this.

The SourceCode.Workflow.Management APIs should allow you to do this.  However, given that the management interface is already done for you in the process management tab, I would prefer to use that.  Basically, I would normally recommend installing a copy of the designer tools somewhere in your production environment as this is mainly for process instance management and debugging.

Thanks for the reply johnny. Will try this in the production environment and check if it really works.