Once the files are deleted, they are gone -- unless Windows has a recovery function (I do not know of one).
I found this in one of TiVos support articles:
So, somewhere in the software is a box you'll have to uncheck if you don't want the original file deleted.
As for the other part of your question, the files don't appear in the recycle bin because the Tivo Desktop software permanently
deletes the files and I don't think there is a way to change that.
If you want to make use of the recycle bin, you have to manually delete the files from the Windows environment, outside of Tivo Desktop.