I'm always a little cautious when updating modules, so I tend to download and unpack the new modules into a 'workings' folder rather than the 'modules' folder... Then I make sure I have downloaded the current (now out of date) module from the server using FTP so I have all of the files that are currently working downloaded too... Then to update the module, I simply drag it's folder from my 'workings' folder on my computer, to the 'modules' folder on the server... This means that the server now has the updated files, and I have both on my computer...
I came across something the other day that caused a little confusion as the 'Date' module needed updating because of some security issues. As there were several other modules that needed updating at the same time, I just downloaded the whole 'sites/all/modules' folder and uploaded the new versions as mentioned above... However, when I refreshed the page, I had a blank white screen.
Blank White Screen
For those who don't know why you sometimes see a blank white screen, or haven't seen it before, it's basically when PHP throws an error and displays it on the screen... However, the server is set not to display errors (often the case on a production server especially with shared hosting), therefore you just get a blank screen with the error hidden... Not very helpful! Mark Jackson explains how you can get errors to show, but for now I'll continue...
The Cause
I reverted the files back to where they were and was going to try again, this time updating one module at a time... However, I still had the white screen... I ended up running a fresh install and eventually was back to where I'd started... It's at this point I'll stress the importance of backing up your site, files and database...
I started looking at the files I had downloaded from the 'sites/all/modules' folder before I'd started updating the modules, and I noticed that the 'Date' module wasn't in the folder... I looked again at the 'Available Updates' page and sure enough, there it was, listed in red with a security update notice...
Then it dawned on me... The reason I had the blank white page was because the site had the same module in 2 different places and therefore the same functions were being called. This caused PHP to throw and error to say that function of a certain name has already been created and you cannot do it again... So somewhere in the site files was another date module!
After a quick search for 'date.module' in the 'sites/all/modules' folder, I discovered that the 'CCK' module had another 'modules' folder within it, that had several modules it used... and it was here I found my 'Date' module....
All I had to do now, was to delete 'Date' from this location on the server, upload the new version, (which I placed in 'sites/all/modules' so it didn't cause any more problems later on), and bingo....
As I said, I hadn't come across this before, so I hope it helps someone else out...