Even if the partition manager is smart enought to modify them, you still wind up with artifacts, which is really, REALLY annoying! I had this problem a few months ago and it took a few weeks/month or so to sort out. It was little things - I had moved a bunch of data files that are normally located in the programs' folder under program files under the root directory to a different partition (makes backups and re-installs of windows easier to recover from) and these links were not changed. So, my Outlook pst file wouldn't open because Outlook was still looking on drive F:, which no longer existed (I combined E: and F: and wound up with a bigger E: partition).