It will ultimately depend on the machine model, and what type of disk you're using.
The majority of rs6k's (that I've worked with) require that the OS be installed on SCSI drives that do not happen to be hot-swappable.
The dominant hot-swap drive technology in rs6ks (assuming you're not using a Shark or something like that) is SSA, and the majority of rs6k models cannot boot from SSA.
The latest and greatest models of rs6k's though are managing to break those restrictions. I don't have any of them, so I can't say for 100% certainty, but I'm sure some models have hot-swappable SCSI, and I'm dead certain that certain models will let you boot from SSA as long as it's JBOD and not in some sort of array.
If you mean just the "hotswap" DASD in say the F50 you are not going to have any issue. Now, if you decide to actually swap the disk, the term "hotswap" just means that you do not have to power down the machine to take out the disk. you still have to do all other normal maint so that you do not break your box. IBM Certified -- AIX 4.3 Obfuscation
If you just mentioned a SCSI hot pluggable hard disk than internal SCSI Hard disk, then there is absolutely no problem. All my servers are using only hot swappable hdisks for their rootvg and is running 4.3.3
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