Dumping a save from GBA VC on 3DS is relatively straightforward. It's been a while, but the first two hits I got on google were for godmode9 and agbsave9, so check those out in the 3DS forums.
Then you'll have to make sure the saves are in the right format for vba next, chances are pretty good they might be already but if not there's an internet full of save converters waiting for you.