Always remove the negative first and put it on last, safest way. For a MH remove the negative from both banks first just in case the isolator is engaged.
Check the negative to the chassis for any problems. Turn on some light switches so that there will be a load. Check for battery voltage with a voltmeter. Connect the voltmeter to a good chassis ground - NOT any cable. If you have 12 to the negative battery post the negative wire or connection is bad. Then with 12V on the positive post start tracing the wiring to the disconnects, fuses or CBs until you locate the problem.
A short on the battery might cause other problems, the charger might not like a short. Other devices might have storage capacity - think capacitance and might not do well with a short. Then a short of that size might cause very high voltage and amp transients which can cause damage.