There is basically no support to do this automatically. The real question also is, what would be required. There is no tool reason either to do this either. Based if you don't there might be impacts on planning, but unless you clearly identify what you can not do, I would question it is absolutely necessary to "merge".


With no data to work with, here my suggestion if you think you absolutely have to "merge". TEST THIS ON A TEST SYSTEM before you use it in prod.

1. Pick one of the project areas to go to. Check if roles and permissions suit you. Add categories and team areas when needed. Administer the project area in case it is necessary to bring stuff over. Reasses what is actually needed. You might have customization data that is not really needed. Trim down and leave behind stuff that is not needed.
2. Work Items. Get the Work Item Bulk Mover UI from the Jazz community. That should allow to move work item data over.
3. SCM change ownership for what you want to bring over, otherwise SCM does not live within a project area
4. Builds - create new build definitions etc in the common project area based on the data you abandon.
5. Plans, Dashboards, reports, try to copy or rebuild them

If you really want to move to a new project area, you do the above twice. Note, if you pick a totally different process, you will likely have to change a lot later.

Steps might require more or less manual work.