Have you checked the alternator belt tension? If the belts aren't tight enough they could slip at low revs and therefore the alt won't charge.
It could also be a blown rectifier in the alternator...you need an auto electrician to check that.
The red handles only disconnect the batteries from the users on the boat. The alternator output is wired directly to the batteries.
If you have a rectifier failure in the alternator it is very unlikely that would lead to the Masse -ve light being activated.
Diodes generally fail open circuit not short circuit.
The -ve masse light indicates that you have a connection somewhere between house bank -ve and the bonding system (ground). The most likely cause of that is something that is 24VDC powered and also has metal parts in touch with saltwater. The macerator pumps in the heads are the usual culprit, but beware of AC devices such as laptop chargers which m
ay internally have -ve connected to ground and that will feed back through the system if you have the original Calpeda A/C pump...that is where the AC ground is connected to the bonding system.
In summary i don't think your alternator issues are associated with your -ve masse issue.
Elyse SM437, the Blue Lagoon, Fiji