biomac--You're the first I know of that links hardware changes with lost incompletes. There's no solution I've read of, but here are a couple of possibly related links.
This link is about problems after hardware changes (can't find a more recent one), so a search for 'firmware' here might lead somewhere useful.

folks on Acquisition forums have seen lost incompletes for months (especially large ones), but they haven't found a solution. Any chance you have some Acquisition prefs on the HD?