They are storing map activation data, so you have a set specific to each map.
I believe that they are also stored in flash memory, and as long as you don't delete them (with the clear flash tool), you do not have to reactivate the map if you remove it then re-install it.
I think problems can occur if you have activated a number of maps (not sure how many) because there is only room in flash for so many of them and the old ones persist. Hence you can then have a problem when installing a new map. This is when you may need to use the clear flash tool.
In response to the OP, my guess is that even if you don't copy them across from your backup, the map will be activated, because they are stored in flash memory also. IIRC they just recreate themselves from there, so you will find a copy of them on your new rebuilt card.