IPad syncing with new installation

I've had my iPad synced with my Mac Pro running Leopard since I've had it.
For one reason or another I've never got around to updating to Snow Leopard despite having a disc partly as I had some incompatible apps, partly as the Leopard system has been pretty stable.
The other day I decided it was time to change to Snow Leopard but removed the Leopard boot drive rather than upgrading, and stuck in a new drive and did a 'fresh' install on that from the DVD.
Gradually recreating an iTunes library on the new drive by adding media files.
Clearly this iTunes instance has never seen the iPad before, but my question is will I be able to connect and backup current iPad installation to this effectively new computer or should I swap the Leopard drive back in to do this?
Also if I run into problems will I still be able to restore an older backup from the Leopard drive?
BTW I generally manually add media files to the iPad, and assume they might disappear if I sync with a new iTunes instance even if I disable automatic syncing in iTunes?
Thanks in advance?

Thanks for the suggestion.
My older itunes folder/library was in a bit of a mess so I wanted to start with a clean slate and repopulate from scratch, weeding out rubbish. I have media spread out on loads of smaller drives some of which does not have correct metadata as I haven't added it, so taking the opportunity to spring clean/tidy up.

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