Forget about charging it from the engine if you want the battery to charge properly. It won't.
The alternator will probably survive a split second disconnect with no problems (do it with engine idling an minimum revs though, where the output is lowest, I think it is the voltage "spike" that kills the regulator pack when it is charging away and all the load is suddenly taken off, rather than actually not being connected to a battery. Think of it as being like your prop suddenly coming out of the water on full throttle, you get the sudden shower of pistons and conrods and £ signs before your eyes!).
But the main problem is that if you charge a nearly flat battery from an alternator it will get maybe 70% charged in a few hours running, but will never reach full charge. Take it out and charge it on a mains charger, for best battery life you don't want a modern starting battery to be partly charged, they don't much like it. If it is a deep discharge it will be less fussy, but you should still take it out and charge it right up.
The same is true of any battery/alternator setup. You can run a battery partly charged in a vehicle and get away with it for a long time, but it will never perform as well as one that has been properly charged. No point having a backup battery in your boat/vehicle if it isn't 100%!
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