Tim, what you have said provides a few clues to the problem you are seeing.
Assuming that someone has not accessed the hidden menu which allows factory alignment of the radio, your problem is not a config issue. If someone has messed with the alignment settings, ignore what follows, because what to do for that is a different answer.
I'm guessing that you are deciding on whether or not the FT817 is outputting power by looking at the power meter bar graph on the FT817 screen or by looking at an external power meter. I would use an external power meter connected to a dummy load to be sure. I'm also assuming that the problem you are seeing occurs on AM, FM and SSB. If there is no TX output only on one mode, then the diagnosis given in this answer does not apply.
For a radio that doesn't have any faults, the kind of antenna you are connected to makes no difference as to whether or not the FT817 will try to output TX power. For a working radio, ff the antenna is bad or missing you will still see TX power output shown on the power meter bar graph on the FT817 screen but the high SWR icon will show.
There are no menu options for the FT817 which can cause output to be present on VHF/UHF and not on HF/6m. Also, there are no options which would cause no SSB transmit audio (and seemingly no TX output power because SSB only has power when you talk) only on some bands. So if there is SSB transmit audio on VHF/UHF then the SSB audio circuitry will be working on the lower bands as well.
Additionally, the only power control for the FT817 is provided by the menu keys under the display, and this sets power for all bands from low to high but does not allow the output power to be turned down to zero or adjusted separately for individual bands.
So your problem is not being caused by incorrectly set menu options.
The FT817 has a separate output stage including final transistors for HF/6m and VHF/UHF. It seems to me that the most probable explanation for what you are seeing is that the HF/6m output stage has failed, and this is most likely (not definitely) going to be caused by a failed output FET 2Sk2975 in the HF section of the PA output module. This device can be replaced but you need a high powered soldering iron and good soldering skills as there is a large area of heat-sink around the device which makes removal difficult.
See this link http://www.ka7oei.com/FT817-finals.pdf for an explanation on how to replace FT817 finals.
If the fault isn't the HF output FET, then fault finding will become more involved and complex.
Also, the reason for a failure is another whole subject. If the FT817 does actually have a fault, I think you should try and determine why the FT817 has failed, for example transmitting using an antenna with a bad SWR, so that you can prevent a recurrence.