Upgrade from 13.5 to 14 with JCEKS keystore in non-default place renders openam unbootable

Repro steps
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• Install 13.5 clean
• Change the JCEKS keystore file path from %BASE_DIR%/%SERVER_URI%/ to something different in the OpenAM console. Move the file to that location on shell.
• Upgrade to 14.

Expected
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• The JCEKS keystore in use gets the configstore and dsameuser passwords.
• .storepass, .keypass and keystore.jceks remain in their configured locations.
• There is a boot.json file in $HOME/openam/

Result
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OpenAM boots after upgrade, but:

• The JCEKS keystore in use did not get any password.
• .storepass and .keypass got recreated in the same path the keystore is, instead of keeping their configured locations.
• There is no boot.json file nor bootstrap file in $HOME/openam. OpenAM won't boot again.