Since there's no if/then functionality in the FTP scripts, if you want it to work both "from scratch" as well as working for later fidsifts, then you have no choice but to do the PUTs every time. They won't hurt anything.

Oh, and: The only reason that I didn't suggest path-speccing fidsift before (The thing Mark showed you that solved your problem) is that you said there was a long pause between the time it tried to execute fidsift and the time it returned the error. I assumed that if it simply couldn't find fidsift then it would have returned the error instantly. Clearly, I was wrong.