There is often a conflict when you have 2 different efi partitions. When you removed one drive while installing fedora you forced the installer to create a second efi partition on the second drive and I am surprised that grub was even able to boot windows initially since it had no reference to it during the initial install.
You can use efibootmgr -v to see what the current boot order is.
You can also use the -o or -n options with sudo to set the boot order or next boot choice.
I would strongly suggest that you merge the content of the two different efi partitions into the one on the windows drive then delete the one on the fedora drive after you have verified that both OSes boot properly that way.
This link might help.