So the plan is to clone the existing and do an in-place upgrade, while this being done, there are chances of updates happening on the existing system with uploading assets and workflow updates. We want to make sure all the active workflows in the existing system is coped to the new instance.
What would be the best way to move all the delta workflow instances from one instance to other? Would packaging the entire /var/workflow/instances cause any issue?
I would recommend you to do a content freeze while you are doing an upgrade in production. When you move content or workflows from 6.4 to upgraded instance then you basically bring in data which has not been in place upgraded. The in place upgrade utility will make sure to update any properties on the nodes which have changed in 6.5 version. So it will not be a good practice to bring content from 6.4 instance after you have done in place upgrade.