You'll know if the CMOS battery is dead. BIOS won't hold time or any settings, reverting back to manufacture date and defaults. If this isn't happening, I doubt it's that.
Some points:
Using a HDD caddy probably won't yield you the same results as plugging your drive directly into the correct interface, due to conversion and that most caddy chip-sets are cheap and simplistic compared to a motherboards south-bridge.
What OS was the PC running that you looked at the HDD on?
Yes you could just grab another HDD and jam that in then reinstall windows.
Yes, Linux could (and should) absolutely work live boot as could any other live boot distro unless the HDD is buggered or the data is gone.