I have been using a dual-boot Windows 7/Ubuntu 12.04 system for a couple of months with Windows 7 on a 1TB Hybrid HDD (Seagate ST1000DM003-1CH1) and Ubuntu on a 512GB SSD (Samsung 840). During this time, I have spent the majority of my time in Ubuntu occasionally accessing files from the HDD that I needed for an operation in Linux. Some time after adding the Ubuntu SSD to the system, I noticed that when I did boot into Windows it seemed like things were running a little slower, but I thought maybe I was just imagining it. A week ago, the HDD crashed during a reboot after which BOOTMGR could no longer be found. Our IT dept said it looked like the disk was now operating too slowly to function and had developed some bad sectors which may have overlapped the location of BOOTMGR.
I am now wondering, since the drive has been replaced and I am restoring my system, whether my Ubuntu configuration may have been related to the slowing of the disk and its eventual death after barely a year of use. If so, I would definitely welcome any suggestions for tweaking my setup so I can avoid a recurrence. One thing I've noticed is that the I/O scheduler for both disks is deadline although I've been told that the optimal scheduler for HDDs is CFQ. Is this something I should change?