Sailboat upgrades. There are several relatively low cost modifications that can be carried out on the boat battery charging system to provide some measure of redundancy and increased reliability. Most of these measures are the result if risk assessing your systems and identifying failure modes. These are my suggestions but every boat is different, so loom at how you can improve your reliability.
A Second Alternator. Install a second alternator on the engine, and this will generally require the addition of a second pulley. Some boats have very tight engine spaces and this may be difficult. The second alternator is for the house battery charging circuit, with the existing alternator being used just for charging the start battery. Each alternator will have a separate positive circuit without any switches or other devices in it. This will eliminate changeover switch problems on alternators that commonly destroy the alternator rectifier diodes, and just as importantly reduces electrical connections to just 2. It also eliminates the accidental (human error) switch operation under load, or switch contact failures, which are both very common. Each alternator will have a separate negative circuit cable running back to the respective battery from the alternator. This provides separation from the starter motor to battery negative, with the main starter negative serving as a backup. This also reduces circuit connections to just 2. It also takes the engine block out of the circuit, and generally reduces voltage drop in the circuit. There is anecdotal evidence that current flow though a bearing also results in reduced engine bearing life.
Separate the Charging System. Separate the charging system from the starting circuit, in the long term this will considerably reduce problems and increase reliability. This process entails the deletion of battery selection changeover switches, and the installation of a separate charging circuit, which may include charge splitting diodes or relays. An emergency crossover switch between battery banks can be installed, however this does not affect the circuit during operations.
Install Separate Negative Cables. Install a separate negative conductor of at least 15mm² (6 AWG) from each alternator case or negative terminal directly back to the corresponding battery negative. This bypasses the engine block and all the cumulative resistances of mountings and brackets. This offers a good low resistance path and reduces stray currents through the block, which can cause pitting of bearings. It also eliminates a single point failure of the main negative connection to the engine block, which if it comes loose, off or fails the spike also blows the alternator diodes as well as causing serious charging efficiency losses.
Replace the Positive Cable. Most installed positive cables are too small, especially if a fast charge regulator is installed. The cable size should generally be doubled over existing sizes. Ideally install a minimum of 15mm² (6 AWG) cable size. I usually take the alternator maximum rating and add 25 - 35% as a rule of thumb. A common problem is that besides having a maximum current going through it with fast charge devices connected or when heavily discharged batteries are recharged, the heat of the engine compartment also de-rates the current capacity of the cable. In most cases a significant voltage drop develops across the cable under full output conditions. This also should ensure that cable connections are also properly rated for the maximum current, a common failure point is undersized terminals causing high resistance and hot spots. This drops charging efficiency and can lead to major failure. When a main positive cable connection fails the spike usually blows the diodes in the alternator.
Starting Circuit. Relocate and connect the main negative cable as close as possible to the starter motor. This maintains 2 connections but takes the engine block out of the circuit, and generally reduces voltage drop in the circuit. These commonly vibrate loose and are rarely checked and tightened. In most cases a new negative cable will be required. All about boat maintenance and sailboat upgrades to electrical systems.