I've started many diesels that sat for extended periods. Some in mothballed ships with diesel many years old. Probably not a problem. Tanks will have some water in them from half full tanks. Make sure you have a good primary fuel filter like Racor. One that separates the water. Add a fuel conditioner. I use Archoil AR6000. It helps combustion and increases mileage of good diesel. I run it all the time in my diesel pickup and got about 10% better mileage. I just started using it in the boat, but get better cold weather starts. Available online.
Add a conditioner, add some new diesel, make sure all linkage moves freely. Whatever additive, make sure it kills fuel bacteria. Leave existing filters for a few hours after the conditioner. No use plugging new filters (if it's going to happen). If you don't have a gauge between the primary and fuel pump, add a vacuum gauge. It should show zero and gradually increase as the filter catches debris. 0-15 or 0-30 (inches of mercury) is plenty. Once the tanks clear up and you buy clean diesel, you'll find you can go much longer on filter changes using the gauge as a guide. Carry extra fuel filters!
My current boat sat for 6 years before I bought it. 2 mains and 2 generators. That's what I did. At the time I used Algae-x and carried extra filters. No problems in 600 mile ocean trip home. I've been running diesels since the late 1950s.