Unraid identifies disks by serial number, so as long as the controller passes the disk through unmolested unraid will just assign them back in the same logical slots, and if you remove the disks, unraid will see that you have more missing disks than you have parity disks, and not start. If you have 2 parity disks and remove 2 disks, unraid will emulate their content so you can replace the disks.
To change the logical slot numbers for your disks, you will need to do a new config. If you select the option to keep all assignments, when you go to the main GUI tab all the disks you transferred over will still be assigned to their original slot numbers, and you can rearrange however you want. The only disks that will be overwritten are the parity slots, so just don't accidentally assign a data disk to a parity slot and you should be fine. Do NOT select the parity is valid option, because it isn't.