Well with not knowing how you have tried to export your files, i maybe going over old ground for you at some point, there are a couple of ways of doing it.
first way
on your old install go to file at the top and then to backup and select it, save the resulting file in a place you will remember, this file will now need to be transfered to your new install, via usb stick or over network or sd card, any of these methods will do.
open basecamp on your new install and again go to file but now select restore and point it to the file you have taken from your old install, depending on the amount of data it may take a while or not.
second way is to select either export my collection, you would do it this way for folders in your collection. or export selection you would do it this way if you wanted to select certain items and not others to transfer.
go to file select export my collection and pick a place to save the file, and then transfer it to the new install and go to file and select import my collection. ( i am guessing this is when your problem occurs)
for the export selection you need to choose what you want to transfer by highlighting the files (routes waypoints ect) and then follow the same procedure.
I hope this helps.
I would of course advise doing this before moving your maps to your slave hdd (the big drive you spoke of) on your new install as i am uncertain as to whether it may make a difference, once the maps are moved it will have no effect on your new saved items but it may on your old files i do not know.