In the recent update Collections has been renamed into Sets, and consequently containing folder as well has been renamed. This was made in preparation for workshop integration to avoid ambiguity with built-in workshop collections. Unfortunately due to change of file paths, the game no longer will be able to read old progress.
In order to perform manual migration, please go to the game directory and copy contents of old Collections folder into new Sets folder. After that restart the game.
Sorry for inconvenience.