I am using the Automation Studio to initiate an Import of a file from an FTP server into a data extension in ExactTarget. I need to keep the file once it is done the Import, however it needs to be named something else on the FTP server so it is not reused. How would I go about doing this? There is a question similar to this on the stack exchange, however it was said to be incorrect by some of the comments. I tried using a File Transfer activity to re-upload the file, however this does not allow renaming (as far as I know).
You can use the move file functionality. Please see below
Once you've imported the file into your target DE, couldn't you import the file to a temporary DE (overwrite), export it with a different name (using not only %%Year%%%%Month%%%%Day%% but also %%Hour%%%%Minute%%%%Second%% so it's going to be unique every time the automation runs), then transfer it to the FTP folder of your choice? I'm not sure of your exact requirements, but it seems like it could meet your needs.
If you're creating the initial import file via an extract activity, then it may solve your problem to simply add %%Hour%%%%Minute%%%%Second%% to your naming convention. I wasn't sure if you're doing that or importing it from an external FTP server.