Is the "new" partition the same, or at least an "Amiga" filesystem? Otherwise you might run into some trouble copying to a fat32/ntfs/nfs partition with file attributes. There's a few scripts on Aminet that would help with this if thats the case. (Thought I'd pipe in, having recently datadumped a 2.1GB drive to an 8GB USB thumb drive to restore to a 40GB drive I was upgrading to. 1 44-pin IDE port, 2 44-pin drives, no 44-40 pin adapters for the other 3 slots..
BTW... it IS possible to use a Subway USB boot floppy to mount a thumbdrive and continue booting from it, but requires some good reading material for the ensuing wait.. ugh..) Did a quick aminet search for that script, couldn't find it. It will recursivly go through a directory tree, and put an amigados script that resets all the protection bits @ the root level. (AmigaOS3.9 seems really picky about that.)