Yes, you can, you don't even need to have same partitions or same cards. I see two important points:
1. You will need to sys.com/make the other card bootable in addition to copying back all the files. Maybe also set partition to active if it's not.
2. Make sure to not only copy hidden and system files, but to also maintain the attributes when copying back.

You can even do it on the same PC, we used to connect the second device as a slave or to the secondary IDE. Partition, format, sys and then from within windows command prompt using xcopy32 (to maintain long file names and use its additional switches /h /k) do the copy.

You could also use a disk imager program (dd/etcher/win32diskimager etc) to clone the entire drive at once and not have to faff about with running sys/worring about hidden and system files/ etc

Hmmm yeah maybe I'll make an image of it and then just write it a bunch of times as needed

if you're just going to copy the files, then you have to make sure the partition is active and the drive is bootable.

if you're going for diskimaging, the old versions of ghost (commercial software) are quite handy.