We have a database server with U2 installed on a windows 2003 server with RAID5 setup. I'm wanting to use Diskkeeper to defragment the different partitions. Has anyone ever ran into any issues or data loss when defragmenting a drive? Are there any dangers when defragging?
No. Except it makes NO SENSE on a properly conffigured SQL Server (if your partitions are aligned, node size is set correctly to the NOT DEFAULT value).
You'll be fine.
Other than defragmenting the filesystem there may be a way of defragmenting the database itself (i.e. how data are stored inside the database files) . The exact procedure depends on the database product you're using though.