I know what you mean. I used to have a piece of software that every time I altered the hardware on my computer, the licence "key" would stop working. I then had to start the program, copy a string of text into and email, contact an outfit in France and wait several days for a new key (another string of characters).
However, in cases like this, I just assume that whenever I would need to re-download (HDD crash, et. al.) they won't be around anymore - Burn it to a DVD - with an extra .txt file with the "key" and voila - I have the same thing I'd have if I bought it.
So, download can work, you just can't trust em. I knew I was rolling the bones when I bought SH4v1.5 from Amazon and fortunately I rolled a hard 6.