Recently I've been working with Ubuntu, installing, reinstalling etc. to get it to work. Finally I decided to use a virtual machine- they are much easier to troubleshoot and work with. So now because I had been installing Ubuntu so that it could actually boot on startup using grub (with the other option to boot windows), I now had a large partition which I needed to get rid of.
So I followed the procedure which you'd think is most appropriate. I transferred all my files (about 530 gb of them) to my internal hard drive to later delete the partitions (I had to delete all partitions and then create a new one afterwards, since there was an error about dynamic disks or something. So I had to get rid of the files on my external hard drive anyway.), and then seeing that about 530 gb of files had been added to my internal hard drive a few hours later, I deleted the files on my external hard drive. Little did I know that a small 0.5 gb (approximate) of files were NOT added to the internal hard drive, these being the only files which I didn't have backed up somewhere else since they were updated so often.
Lesson learnt...
Check that every folder and file is there, and that all folders are complete. You could even check that the folders contain the exact number of bytes as the other copy of the folders. It's a less than 5 minute effort which will ensure you to not mentally 'break down' afterwards when you've realized you are in the reality of one of your most dreaded situations.