Alright, the tileset image getting cropped would mess up your map since the cropping affected the indexes of most of the tiles. In addition there appears to have been a change in the tile size used by the tileset, causing all your tile rects to be misaligned.
The easiest way to restore the map should be to revert to a non-broken tileset image.
It is however impossible for Tiled to mess up your image like that, since it does not write to tileset images, ever. I’m sorry if you lost your work on the tileset, but the image must have gotten messed up some other way. Keeping backups is a good idea, regardless.