Just some ideas...
Are the Mastervolt
lithium batteries disconnecting on overvoltage and frying the alternator?
Have you programmed your alternator
regulator for
lifepo4 batteries?
What
regulator? If
Balmar, see
Marine How to Programming Balmar Regulators.
IMHO lifepo is not just
plug and play even if you buy one of these packaged batteries with a BMS inside, you have to look at the entire system. I would want an external relay controlled by the BM to disconnect between to
lifepo4 and the alternator to protect the batteries, but you should also have a simultaneous Alternator field wire disconnect to protect the alternator, unless you have an FLA
battery directly connected to the alternator output, ready to accept the
power. Otherwise you will get a dangerous condition and an expensive
repair similar to what you experienced.
Not all packaged Lifepo4 + BMS packages have the ability to control an external relay and that is a problem in my opinion.
Disclaimer: I have not yet built or operated a lifepo4 BMS system. I have been reading up for several years.