@dvlzplayground
do you remember if at any point you did a 'partition' process? that would explain why your data is missing...

cos if the partition table has been altered, usually data is lost.
so far, in my experience, only PartitionMagic (windows) can make changes to partition tables and keep the data.

cloning also means if anything happens, you can immediately swap the clone drive with the faulty drive.
when I have the means, I would set up a nightly clone, so even if the drive fails 100% ... i will only lose 1 days work.

Time Machine is slightly different, cos you backup every day, so you can go back to (for example) Dec 2009 and get back a file from that time, even if you deleted it yesterday.