After an email received from Lost Dogs UK yesterday, I contacted Network Rail to find out their company procedures with regard to missing dogs.

I have been informed that the company policy states that any
contractor/employee who finds a dead animal on the track or embankment
should remove all identification eg collar and tag etc., and bury the animal
on the embankment.  They are supposed to pass information and the id onto their area office for them to make contact with the owners. 

If a contractor/employee finds an injured animal they are to move it from further danger and contact their area office who will then arrange for the RSPCA to attend.

I raised the question of microchipped dogs without any form of other
identification, the lady was most helpful and will pass this onto her
superiors for answers.  They have taken my name and address for the reply.  Will let you know when I do get a reply.

The lady also pointed out that its an offence for any person/s to be on the
rail tracks or embankments, its classed as trespass and people will be
prosecuted.  If anyone should sight their animal nearby or on  a track they
should immediately contact the following number 0845 7114141 and not attempt to approach the tracks themselves.  Missing dog alerts can also be given to the same helpline number and it will be passed onto the relevant regional
office.

Hope that clarifies a few things.