Can you try moving the .jpg from .../cuteTube to .../cuteTube/.thumbnails? (Note the dot, as in cuteTube slash dot thumbnails.) Then start CuteTube and check if the video reappeared in Archive.

I have a different problem. A lot of videos I download play fine as Archives in CuteTube but do not play at all in Media Player. Why? It seems completely random (or at least I have not found any pattern yet), but it is consistent: the same video either plays fine or not.