BB,
If the Si sonar is messed up the Di sonar will be too.
No, this is not the 800kHz washout issue; it is something else.
Do you know of anyone who has a Humminbird Si model unit that you could test your 999 unit on their transducer and their unit in your transducer? This is the only way that you will know whether the problem is in your unit or on your boat/transducer.
To reload the current software you would need to load an older version first and then load the current software again. I would encourage you to contact the Humminbird Customer Service folks first before doing this. The reasoning being that if something goes wrong during this process they may be more likely to cover it under warranty. If you need for me to, I can send you the software versions to do this but I encourage you to give the Humminbird Customer Service a chance first.