No, HX3 is a fixed firmware part. We do not support custom pin usage as described in your requirement.
Is there any firmware way from the Host side to disconnect and reconnect?
If there’s a way to do this via software from the upstream device, that would be ideal. I know the upstream device can be used to change the configuration settings stored in EEPROM, and we’re already planning to figure out how to do that from our in-system motherboards. It would be great if there’s some related way to reset individual downstream ports.
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The ideal way to realize this is to set the soft reset in your device. The host send the vendor command and your device wil reset after receive the command. There are no way the reset the hub downstream port.