I have my 5d3 set to continuous file numbering and all is well (or was well). I was up to file number 900 or so. I plug my 5d3 in to my mac at work and I noticed that the file numbers reverted back to zero. As I shoot now the file numbers are continuous. I formatted the card, removed the battery and it's fine.
I shot some more images and imported to my mac the same way again, but this time the camera kept the file numbers and did not revert back to zero.
Is it normal for this to happen? I never affected my 50D.
I had to use image capture to get the files off my 5d3 because the EOS utility at work is not current and won't work with the new 5d3.