Hmm, do I post this... First, Kentucky is COMPLETELY right in his post and that is good info, and I agree with the end suggestion of warranty claim. Everyone should follow that advice (it's conservative and sound), but I have a couple more safe suggestions you may try but the one at the end is completely at your own risk. So...
Well - some of us have already braved the "shade tree mechanic" side of our personalities in modifying or investigating the hidden PFM in the Honda Clarity. Sometimes we tread the line of voiding warranties. I installed a custom audio system, took the dash apart to clean the instrument cluster cover (because my dealership needed two weeks to get the part and wanted the car for two days, and well - it was a cleaning, something not all technicians do well). Hmm, currently messing with hardware hacking the ANC module to make it analog only and not digital... And then there is that android device disguised as a stereo head unit.... So, tread farther at your own risk, beyond here be dragons... Everyone's Clarity is under factory warranty - so this may meet the definition of insanity.
Provided for your edification only:
To reset the head unit you actually have 3 "levels" of software debuggery built in and a 4th you can "create". If you own an android phone you are already familiar with at least 2 of them.
1) As suggested above, you reboot the head unit by holding the power button for 5 seconds and answering yes to the restart. Your head unit actually does this on it's own about once a day during the night if the car is off. However, it can help here since you said the Navigation comes back every couple of days before disappearing. But I don't think this would permanently fix your problem give that it likely will happen again so....
Have to say here that I have experienced the EXACT same thing, but not for the same reasons. I know what I did to break it and then fixed it myself as the dealership wanted to just swap the head unit for a replacement. And I had the navigation screen so tricked out with themes and icons (airplane for one) that I didn't want to surrender just yet.
...now back to the story..
2) Next is to try a Reset to Factory Defaults. This will reset the head unit using the factory install whitelist and vehicle configuration/customization file from the OEM (Mitsubishi). This is actually pretty safe to do as it is a "user" feature enabled for the Honda device. But you will lose all your customizations (not radio stations, that's saved elsewhere) but things like lane keeping tolerance etc will go to defaults. Steps:
Reset all the menu and customized settings as the factory defaults.
Select HOME.
Select Settings.
Select System.
Select the Others tab.
Select Factory Data Reset. The confirmation message will appear.
Select Yes to reset the settings.
Select Yes again to reset the settings. The confirmation message will appear.
Wait for it to reboot completely and test.
3) Disconnect the 12V battery negative for 10 minutes (car shut off, or DC-DC will power things). Then reconnect and the Infotainment should prompt you to hold the audio power button to reset the system, if not unplug for longer. This is unplugging your computer, but not a big deal. You may get lots of christmas lights on your dash after, but just drive the car for 20 seconds down your surface street at 20-30 mph and all will clear out.
***4) Launch the bootloader/recovery - software update subsystem. This is an XDA type thing. This is something anyone who has rooted an android device will understand and may love. However, here be dragons... I only post this because I HAVE done it and survived but you should know you can brick your headunit here. This can give you some very interesting and powerful access to the HU. But again, unless you know what USB Sideload ADB is, stay away from any option other than the "Factory Reset" But just so you know, this is also where if we ever find a software update image - it would go.
Follow instructions here below to create a USB thumb drive that will trigger the software update boot loader to launch. You do NOT need to be Honda Hacked for this to work.
http://www.autohack.org/how-to-recover-your-system-if-it-fails-to-start/
Once you do this and everything reboots (which will take a while so make sure you are NOT on accessory mode, have the car ON so it doesn't accidentally time out and power off), things will look very weird. The HU color scheme will be wrong and some things just won't work right BUT if the Navigation was going to be fixed, it would be by here. After doing this you need to follow the steps above (see option 2) in the USER factory reset to get things back to "as delivered" from dealer look and feel. Then you re-do all your customizations from there. If you brick your HU, then well, just take it back to the dealer as they were going to R&R it for the Navigation glitch anyway. However, DO NOT LET THEM DO what they call a "HARD RESET" where they take the battery cables (12V) and short them briefly. This works on a lot of regular cars but causes issues on the Clarity and as far as I have found is not in the Clarity maintenance procedures manual. They did that to mine and, let's just say it took me a while to get things back to normal.
I am not responsible if you break your car here. I have just become annoyed with service options at my local dealer. However, I have found another dealer that is not far way and may be better trained to work on this car. So my "hacking" may no longer be required/justified. As a side note for the now intrigued, yes - Honda Hack has it's uses. But be advised that Honda knows about it, has a service advisory to it's dealers about it, and well - tread at your own risk, the HU is about $3500 plus the service visit to get it installed out of warranty if things go south.
Cheers,
Cash