Does he have to have boots on is my first question. If he does then you need to find some that don't rub and keep them scrupulously clean so there's no dirt, sweat, or sand to rub and also so any infection isn't being reintroduced to his skin. I used to use polo bandages on Jim as he was hard to fit boots to, they were soft and easy to wash on a highish temperature after each use but you do have to know how to put them on properly.
I wouldn't be trying to remove scabs, you end up tearing the skin at the edges and making them worse. Instead keep applying a suitable cream and wait for them to soften enough to come off by themselves.
If you're worried about it being the start of or triggering LV then speak to your vet tomorrow, it's definitely a case of prevention being better than cure.