Wow you have a very messed up partition scheme there. You only have 3 gigs for your root fs, but 16 gigs for swap. If you use gptarted to DELETE a partition, then yes, everything in it is gone. It can also resize and move them though, and that does not destroy data ( unless something goes wrong ).
It sounds like you need to just reinstall. I'd suggest just installing to the new hd all by itself, get the system working, then plug in the old drive and pull off any data you want to save.
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