As Rob says in the above
linked thread, the Ignition Module Arduino (IMA, I just created a new TLA

) is looking for the 0.5V delta between the voltage measured when the master switch is first turned on until the engine is running and the generators have transitioned to the B-generator powering the aircraft bus. You must run the engine faster than 2500 RPM for a few seconds for this transition to happen. The IMA will stay in this "actively sensing mode" until the 0.5V threshold is crossed. If that condition never happens then the SBB +5V signal to the HIC is never deactivated.
If the initial EarthX battery float voltage is too high to allow the 0.5V delta to be sensed by the IMA, because the battery was recently charged (either by a battery charger or after a quick turn-around and engine restart [fuel stop, YE flight, etc.]) then I would say the system is working as designed. This condition would be indicated by a WHITE HIC LED. Maybe this is not as good as it could be, but it is within the parameters designed into the current 7.3 IMA version.
The previous IMA version (7.0) would time-out after 60 seconds and this caused many "no start" and "my fuel pumps don't work" situations. There was even a student pilot who was "stranded" at a very remote airport and the flight school flew someone out to rescue him, they "saved" him by activating the Emergency Backup Battery switch to start the airplane.
This is one of the reasons I designed the Diagnostic LED into the -2 version of the HIC module. If the HIC LED stays WHITE after the generators have transitioned then, for whatever reason, the 0.5V voltage delta threshold has not been sensed by the IMA and the +5V SBB signal is still being sent to the HIC Module. If this happens then the Fuel Pumps WILL continue to run after shutdown. What was Microsoft's response to this kind of unexpected behavior, "It's a feature, not a bug"
If the HIC LED is YELLOW (indicating the SBB +5V signal is NOT being sent from the IMA to the HIC Module) and the Fuel Pumps continue to run after engine shutdown, I would suspect the MOSFETS in the HIC Module have failed in a Shorted closed-circuit condition and continue to tie the A-generator and B-generator busses together. This has the same effect as having the Emergency Backup Battery switch activated. The fix would be to replace the HIC Module (or the HIC Module MOSFETS). I can't think of another condition that would keep the HIC MOSFETS active when the SBB signal is not present (YELLOW LED). If this happened then the fuel pumps would continue to run EVERY TIME after engine shutdown, not just occasionally as the OP said is happening in the original post.
Note: the EarthX battery has a very low self-discharge rate and doesn't need to be charged as often as a lead acid battery. Unless you are updating the EFIS or testing lights with the master switch on for longer than about 15 minutes I don't think a charger needs to be connected at all. Read EarthX's recommendations here,
https://earthxbatteries.com/our-batteries/battery-charging/
Hopefully, this information helps you make an informed troubleshooting decision. Perhaps everything is operating "as expected" and you don't have any failed equipment.
PS, I no longer work for Van's Aircraft and this information is based on my own knowledge and experience.