This is embarrassing, I was downloading the files for the secret recipe, then though I moved to the /log directory. Typed "rm *" and deleted every file in there.

I uploaded the file 11_Secret_Herbs_And_Spices.txt to the CSEC Drop Server but responding to the email says "Mission Incomplete".

I can't go back and complete any of the old Entropy missions because it says a mission is still in progress.

Does anyone know how I should proceed or should I start a new game?

The file 11_Secret_Herbs_And_Spices.txt is not the file you're looking for. Just saying. :)
Only 2 people have half of the receipt...

I found this out the hard way. The question is, do I have to start over because I deleted the files?

As far as I know you shouldn't. Just look around in the files for hints. :)