You have to extract the emunand from the SD and then reinjet it in the new sd. The emunand is in the unallocated part of the sd, starting fron sector 1.
You have touse dd on linux to extract it(search in the forum for more info), or a port of it on windows (i.e. bbcopy). For injecting the emunand you can use emunandtool after adding the initial dummy sector as you did when you started installing the cfw injecting the nand.bin in the GW emunend (with dragemunandhere.bat).
The right sequence is:
- extract emunand
- backup sd content
- prepare new sd with gateway (format emnand)
- inject the cfw in new sd with emunand tool after adding the dummy sector
-copy backuped sd content on new sd
-done -> launch your new CFW