'like in Repo Man, for example, where the intro sequence stated that four years have passed between the present and the end of S3 (2008), even though it has actually been five years, if we count the year Dean spent with the Braedens – and in others they seem to remember the correct timeline.'

I don't think they were very specific with when the flashback took place, just that it was four years ago. Some fans believe the flashback was set in S3, some in S4, depending on whether the 'missing' year is counted or not.