When a killed vaccine is used in an outbreak situation including FMD - and FMD vaccine provides solid protection from infection with one dose of the high potency vaccine - there are occasional instances when either the vaccinee has been exposed to virus just before vaccination or in the first few days afterwards.
If the vaccine is given around the time of infection particularly in the few days after exposure, it can modify the infection. The immune response to the vaccine somewhat precedes that to the virus which is more slowly getting underway early in infection because the vaccine is a relatively large dose of highly immunogenic adjuvented virus protein (the structural virus proteins but not the non-structural virus proteins are included in the vaccine). The high potency vaccine is designed to produce a good level of protective anitbody by 10 days after the inoculation is given.
If the incubation period should be changed by prolonging it, or the exhibition of any symptoms and signs should be diminished, and virus clearance delayed, this is quite normal in human and animal virus infections when killed vaccines are used. It is not an attribute special to FMD vaccine. To suggest that "this is what happens with foot and mouth vaccine" just displays ignorance of infectious disease in general and vaccination in particular. (This is one of the problems of scientists in labs; they usually have no specialist training generally in infection or virology, nor any experience in the field. Their focus is narrow upon their subject of research, valuable illuminating and relevant though this might be).
If vaccination was used on a farm where there was - unknown to the vets- infection early in the incubation period, or exposure a few days after vaccination so that a few infections modified by vaccine occurred, this farm would be detected on screening during surveillance. All animals infected by the virus make antibodies to the non-structural proteins and so the the antibody test to these would be positive (The test is negative if the animals are only vaccinated as they can only have antibodies to the proteins presented in the vaccine, the structural proteins.). The test for anitbodies to non-structural proteins is validated on a herd or flock basis.
All the animals on the farm where any tested positive to non-structural antibodies would be culled as the premises would be classified as an infected premise on screening. (As per EU Directive Article 57 paragraph 3 p 29)
Even so, the virus infection would be limited on that farm. 5 days or so after vaccination antibodies to disease have developed so the virus cannot continue the chain of infection. It will not be able to spread -neither on that farm nor into the vaccinated neighbouring farms.
It might be thought then, that killing the animals on such a farm to be entirely gratuitous. However FMD can give rise to an infectious carrier state particularly in cattle when the virus may be shed from the oropharynx intermittently making it hard to reliably detect such animals. The antibody test to distinguish animals infected by virus may not be relied upon to clearly discriminate infected from vaccinated animals on a single animal basis with reliable accuracy in every individual case. Also a farm on which there have been infections must be cleaned and the dung appropriately disposed of.
FMD vaccinated animals on uninfected farms are the ones that should not be destroyed. The possession of protective neutralising antibody prior to infection changes the whole outcome if a vaccinated animal should be exposed to FMD. If a vaccinee should somehow come across the virus (which is unlikely in a vaccinated herd unless there is exposure to infected deer or fomites) it is either completely protected against infection ( the commonest case - which is why FMD vaccine is so good) or, if infection should occur, it would be limited and the animal does not become an infectious carrier.
Antibody to killed vaccines will eventually fade, and become undetectable, so that if FMD remained in the environment vaccination would have to be boosted perhaps annually or maybe more frequently in pigs. In actual practice of using FMD vaccination to control an outbreak this rarely prooves necessary as the infection has been eliminated by one round of vaccination.
( In poor countires where FMD is unchecked infected animals can have complications and sustain injury such as myocarditis - particularly associated with serotype O - and oxen for example can be rendered useless from this complication of FMD infection. Vaccinated animals do NOT sustain injury from myocarditis.)
The rules in the UK on FMD vaccination have clearly been formulated to make it as unlikely as possible that we should use vaccination. They are bureaucratic rules to protect the UK and EU meat industry. Unfortunately, the stakeholders meetings on the subject of vaccination held around the country took place not to consult and listen but rather to be able to say that consultation has taken place. There is no obligation on the officials to take any notice whatsoever of anything said or submitted by those who disagree with the policy.