That is a severe error to make to have your downlds going to the program folder. Yes it will have deleted your previous incompletes. Unfortunately there's not much that could be done about it now. At best, you could try using a file recovery program, but you'd also need to recover the download.dat file & not only the incompletes. Without the downld.dat file the incompletes won't be recognised.

In future, make sure you do not choose your program folder as your downld folder. Best to have them in totally different directories a reasonable distance apart or better still, a different partition/HDD.