Are you sure this isn’t just the pantograph passing through the neutral section? They have these on long runs where the power is supplied from different sources (resulting in sync issues). There are circuit breakers at these points which on some trains makes a very loud ‘clunk’, which stops the train trying to draw current through . The other type of ‘clunk’ you get on some trains (although not the ones you are describing) is the pant going up/down on combined AC/DC lines.