You're not going to hurt either your Ubuntu or Windows systems by exchanging drives, other than the fact that you're going to be handling the drives a lot more than they need to be, and if they're mechanical drives, as opposed to solid state drives, they will probably wear out a lot quicker. You are able to load both operating systems on the same hard drive if that's the only reason you want to swap drives. This is called dual booting.
To accomplish this is extremely easy, you will want to install your Windows OS first (due to Window's Boot Record tendency to overwrite Grub). Once you have Window's installed you can open disk manager, and resize your disk to allow for at least 50GiB of "unallocated" space. Once this is complete reboot your computer and startup into Ubuntu. Click "Install Ubuntu" and go through the instructions for setup. When prompted for which disk to install to, make sure you select "Largest contiguous free space". This will ensure Ubuntu installs to the "unallocated" space you created using Window's Disk manager. When installing Grub, Ubuntu should detect your Windows OS, and will display this information. Go ahead and install Grub, when you startup, there will be an option in Grub to boot Windows. Complete the installation instructions, and viola! You now have a dual bootable system with both Windows and Ubuntu.