Re: fstab irrelevant?
Ah - that may well be why the installer can't recognise it.
Do you not have sufficient SATA headers for them both?
In any case if your intention is to install Ubuntu to the new disk, you could just disconnect your old drive completely and plug the new drive into the SATA header it was using. Once Ubuntu is up and running on the new disk, plug the old one in using the doohickie and copy whatever settings and files etc. across as required.
Just a suggestion based on how I'd tackle it - at least with the old drive disconnected there's no chance of accidentally overwriting your current install
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