Yes. Something must be wrong, else it would be working. ;)
The updates are always created in such a way that you can continue your old progress. It's absolutely not necessary to re-start after an update.
What system are you on? Windows?
Are you copy&pasting the entire content of the save folder, including the .global file? If you did it correctly, you should have "load" as an option when you start the game and see your progress in the save slots.
My best guess would be that you transfered saves without the global, and afterwards started a new game to create a save file in the those save slots, which caused the old save to be overwritten. Creating the new saves FIRST and then copy&pasting the individual saves from your old version over to the new folder also works as an alternative way to get your progress, but copy&pasting the entire folder content should be faster and easier.