Strange, no problem with mine. I think I had this before sometime ago and went to downloadable collections and re-downloaded them. I think I had to do a delete app and re-download app or perhaps an update app - so long ago I can't remember. (I really must make notes when this sort of thing happens!) I just checked and the ones I have in downloads don't show in the available to download collections so if yours show up there it would seem they have been cleaned from your computer. There should be no charge for downloading ones you already own - certainly if you remove them using manage disk space it says you can get them back for free.
You could try clicking on manage disk space (top right near your points in the classic view). It might just kick it into picking all your downloads up. Or try clicking into jigsaw jam or daily challenges. You never know what will fool it into giving you back your jigsaws. Just a quick question are your points showing OK?
I have noticed there are suddenly a whole load of new collections available. I don't know whether they have got rid of some of the old ones - there don't seem to be many not labelled NEW.
Good luck MJ can be very frustrating but hey its free