Summary

Customer faced this issue on his instance and we could reproduce this on a clone of his instance as well. 
See replication steps below :
To reproduce :
We edited the XXX Standard Workflow Scheme with say 20 projects
We expected the change to remain as is once we acknowledge the change
But the workflow scheme screen that appeared is titled "Copy 3 of XXX Standard Workflow Scheme " with 6 projects

Steps to Reproduce

1. Go to View Workflow https://xxxx.atlassian.net/secure/admin/ViewWorkflowSchemes.jspa
2. Click on the "XXXX" row of worflow scheme and click "edit"
3. After completing steps - we expect the edit to reflect on the main workflow scheme but it shows "Copy of XXX" workflow screen instead when complete. It seems to split the workflow

Expected Results

Workflow Scheme is editted and reflected correctly instead of creating a new workflow with a name "Copy of XXX"

Actual Results

The final screen after workflow scheme edit shows "Copy of XXX" with say half the projects and original XXX workflow has some projects. Eg XXX originally has 10 projects then after edit XXX has 5 projects and "Copy of XXX" has 5 projects
 

Workaround

None