Users which had deleted role (e.g. ‘role_1’) on other sites will be shown by WordPress with role ‘None’. If you look at such user custom capabilities you will see ‘role_1’ between them though. If WordPress does not find some permission ID between roles, it counts that it’s a custom capability directly assigned to a user.
So if do not delete such capability from a user, user will get it as a role back in case a role with same ID will be added to a site later.
It’s a current state. I see that some enhancement are desired here.