Hi,
If the correct place is as shown in the photos above, then I had quite a lot of corrosion around those areas so in theory it could have simply corroded away. I doubt it though, with thin metal I'd have expected to see the imprint underneath or the remains of a partial stamp on top, but nothing that I can recall now.
I very much doubt Lotus painted their chassis with blue paint, your theory of a chassis change and extra paint by the owner which he then covered over with black sounds the most reasonable explanation.
If the car was used in the UK on our winter roads then it's not unreasonable to have a replacement chassis regardless of the mileage. When I looked at mine in the early 90s the amount of corrosion was pretty bad, and that was on a replacement chassis which had probably only done 25-30k between 1978 and then. Maybe your car was similar and the previous owner decided he didn't want to do the job twice !
Brian