Folks, the "odometer" is not the issue; the "speedometer" is the issue because on vehicles sold in USA the primary units are miles and Canada requires it to be marked in kilometers. Now it's probably the case that the km are present in minuscule hardly-legible numbers on the US instrument cluster, which is normally enough to satisfy the legal requirements, but perhaps someone wanted to do the job "right" and get kilometers as the primary display units. That's not something you can change by software ... it's physically printed on the instrument cluster.
The odometer gets affected because if you replace the speedometer, you replace the odometer ... it's part of the same assembly.
By the way, some cars sold in Canada do not have the US units printed on the instruments at all ... the speedo in my '96 Passat was metric only, same as the mainland-Europe instruments for that car. I do not know if the reverse might be the case for some US market cars.
Anyhow, IN THEORY, the mileage on the original odometer should have been recorded at the time of instrument cluster replacement, and IN THEORY, a sticker should have been affixed to the left door jamb indicating what that original odometer reading was, and IN THEORY, given that the work was done at a VW dealer, it should have been logged and associated with that VIN in VW's computer system, and IN THEORY, answering that question about whether the odometer was replaced with "yes" should prompt additional questions about how much mileage was on the car at the time of odometer replacement and what's on the current odometer right now, and IN THEORY, that's the number that should be used for buyback purposes. So, IN THEORY, that's how it should work.
In practice ... Who knows. I don't recall ever seeing this come up before.