If vscsi3 was only being used for these disks you could do the following.

rmdev -dl vscsi3 -R

Then use a DLPAR action to remove the vscsi adapter from the LPAR, and then use the save option on the HMC to save the updated profile information.

Otherwise, remove the vscsi adapter from the partition; stop the partition; activate the partition and use the command above to remove the disks from the configuration.

I assume you mean by that you have run the command rmvdev -vtd vtXXXX for each of the disks, not that you have just removed the LUNS from the VIO server.