There is usually (always?) one Sound in a signal flowchart which is highlighted. Sometimes it seems to be the "original" Sound, but sometimes it happens late in the signal flow.
The Sound that is highlighted in a cyan color is the "replaceable input". To select a different Sound as the replaceable Input, select it, go to the Action menu and select Set Replaceable Input. In the Sound Browser, the Timeline and the Multigrid, a Sound with a Replaceable Input is marked with a cyan, right-pointing arrow.
This is a way to mark what you consider to be the "input" to a complex signal flow graph (since it is not always necessarily the leftmost Sound in the signal flow). You can find more details in the Index of Kyma X Revealed (in the Documentation folder in the Kyma folder) under Replaceable Input.
Save As... to try and rename a Sound, the resulting dialog box says "Save this Sound without overwriting the original Sound?" but there is no option for saving the Sound under a different name.
To rename a Sound, select it and press Enter; then type in the new name. At that point, you can do the Save as and save without rewriting the original.