IF you copy ALL the contents of emule's Temp directory into your aMule's Temp dir, then it will surely continue your eMule downloads. What's more, instead of copying those files (or moving thme), i you upgrade to rc3, you can use eMule's Temp directory as aMule's Temp directory. BUT, the Emule Temp directory must NOT be on an NTFS partition.
Greetings!