Swapping 80A fuse link with 100A fuse

What do you mean by "100 amp setup"? Are you replacing the generator too? If you have an 80 amp fuse, you likely have about a 60 amp generator. 60 amps is WAY more than enough to run everything on the car at once. If you install a larger 100 amp fuse and about an 80 amp generator, you are going to get the exact same amount of current from it. It's not going to charge the battery any faster; it's not going to run the power windows any faster. You won't notice any difference at all. The only time you will exceed the output of a 60 amp generator is during a load test on the charging system performed with professional equipment. During that test, it is possible for the larger generator to produce close to 80 amps. THAT is when the 80 amp fuse would blow. It is designed to be the "weak link in the chain". If you replace it with a 100 amp fuse, now the rest of the wiring becomes the weak link. The generator can overload the wiring and the fuse won't blow to protect it.

If all you are replacing is the fuse, and not the generator, it will not adequately protect the wiring. In the rare event two of the six diodes inside the generator become shorted, that puts a direct short across the battery. The 80 amp fuse will blow instantly to protect the wiring. A 100 amp fuse will take longer to blow and could result in the generator's output wire melting first. Beside having to replace that entire wire, it could melt the insulation on the other wires next to it in the same harness. That's a lot of misery and no benefit for not using the right fuse.

Perhaps I misunderstood your intentions. If you're leaving your old smaller generator on the car, that's fine. In this case the circuit will still be protected with the 100 amp fuse that you want to install. AC generators by their very nature are incapable of putting out more current than they were designed for so you're not going to a blow the fuse that way.

The fuse is really for in case two diodes short in the generator. Those are one-way valves for electrical current. Two pairs of three diodes are all that stand between the battery positive cable and ground. If any diode shorts, you lose two thirds of the generator's output capacity. If two diodes short, one in each group of three, you will have a direct short to ground. THAT'S when that 80 amp fuse would blow. Your new 100 amp fuse will blow just as fast so you'll still be protected against melted wires.