MattS:
I have around 12,000 products
Sorry I hadn't read your original post properly, had you changed any files before it would not work( I am sure you didn't but lets rule out the obvious ) if you hadn't changed any server side files than as you said it will be a server issue with your host, 12,000 products may eat alot of php's memory and your host may be stopping this thus you get a '500 Internal Server Error', what has your host said ?

Have you tried to download it to your temp folder on the server and ftp from the server ?

Had you increased your product count when this happened say 10,000 products to 12,000 products, if so again this would show a memory issue ?