I thought I would answer my own question for future reference:
Resetting all state in Wwise can be useful to avoid subtle problems. The SoundCaster in the Authoring Tool has this functionality, but it is not present in the API as of v2013.
It requires:
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unregistering all GameObjects,
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resetting all state groups (state groups are global),
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resetting all global RTPCs
The reset can be done in two ways:
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Shutdown and reinitialize, reload banks. Slow, but works.
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Manual reset:
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Unregister all GameObjects,
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load IDs of all state groups from Init.txt, set them to 0u ('None' state)
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load global RTPCs from SomeBank.txt, reset all using ResetRTPCValue()
I had an idea that reloading Init.bnk would work, but it doesn't.