Click sync so you get a list. Minimize. Restore and it will switch back to home. At least it was for me today 😃
I see what you describe here when I do not select a Handheld before minimizing the sync window.
In this scenario, can you provide a collapsed Action Window as well as a collapsed sync to avoid the extra step through the sync window to get home (i.e. you could remove the sync header's back arrow)? Similarly, when Sync Handheld first opens, provide a minimized Action Window. That would be consistent with the way other Action Window submenus behave upon opening and minimization. I think the fully expanded Tag window is the only exception, where in this case you have to restore or close the Tag window to find a way back home.
If I click sync, select a Handheld, and then minimize, everything remains perfectly logical for multiple cycles, as is. There is always a way to get directly back home (though the return arrow is currently needed after first step).