The batteries may have been drawn down below the Magnum emergency cut off voltage. Both inverting and charging would then not work. See "Possible Cause
" below for what to do.
...it started to work fine. Now Magnum inverter control blinks red fault and batteries are not charging on shore power. ... No documentation for the inverter.
Post the model number of the Magnum inverter/converter/charger. Or search for "Magnum nnnnnnn manual". There will be a table in the manual that will tell you what the blinking light means. That will help you decide what need fixing.
Also the generator will not start even when using the boost. Assuming that the 4- 6 volt batteries are no good. Can we charge them using a charger without doing any damage to anything else?
The batteries will continue to discharge, and after time will loose capacity to be recharged. Generator will not start using dead batteries. Boost switch may not work if house batteries are dead.
Starting the generator will not charge batteries until the Magnum issue is corrected.
The RV engine alternator may charge them partially. Using the alternator may raise the battery voltage enough to restart the Magnum.
The inverter will not produce 120 volt power without 12 volts from the battery.
Shore power may still work OK, but 12 volt appliances will not work.
The batteries are not necessarily defective. There are many possible cause of charger shutting down.
You can use any high quality portable automotive charger to charge the batteries. Some must only be used while attended, some are smart chargers and will work unattended.
A 10 amp portable charger may take days to fully charge the batteries. A 30 amp charger will take about 1/3 as long, but still may take more than 24 hours to fully charge a large battery bank. Have patients?
Did you run the refrigerator using the batteries and inverter?
In this case the batteries would run down in 1 to 2 days. Magnum inverter would do emergency shut down. It will not invert.
Other 12 volt appliances may have continued to discharge batteries until the Magnum charger also did an emergency shut down. It will not charge until battery voltage is brought back up.
Use a portable automotive charger to bring battery voltage above Magnum cut off voltage. (May be 11.5 volts.)
Jump start the generator or plug into shore power. Magnum will start charging again and at some point will start inverting again.
Continue to charge battery bank for at least 18 hours. They may benefit from24 hours charging.
Running 120 volt appliances using an inverter and a 12 volt battery bank requires a large battery bank, or it will only work for short periods before recharge is require.
Lots of thing to learn and possible performance issues. Google Using RV inverters.
This link seems to cover pretty well.
I wish you good luck and happy trails ahead!