It's common practice to keep drivers updated. It's hardly "messing" your system. It's maintenance. If a driver has undesirable effects, there is commonly the option to roll back to the previous one. If Lenovo issue a driver through system update, you can't really blame a customer for installing it.
The problem with this issue is once you have 6.2.1.1400 installed, you have a timebomb in your system. The Lenovo provided driver package automatically wipes out your hard drive as part of the automated uninstall when a newer release is installed - whenever that may be. If you check the release history, Lenovo term the update to 6.2.1.1401 as an 'improvement' to uninstall with no reference to dire consequences of uninstalling 6.2.1.1400.
So, Lenovo kept very quiet about this issue. I suspect it's only affected a minority of customers unlucky enough to have installed that particular version before it was updated. It is a sad indicator of Lenovo's lack of concern for customers that it took a third party to come up with a fix. Lenovo still don't provide a tool to clean up the old driver.
Of course, before you install updates, you should have a full backup so in theory, nobody should permanently lose data if they follow Lenovo's instructions to the letter - but it doesn't mean it's a quick job to recover an entire system.
I was using the Lenovo provided ThinkVantage Rescue and Recovery tool. As an afterthought, I also set up Windows Backup to run to a fileserver. The restore using the Lenovo tool left me with an unbootable system both times I tried it so good job I wasn't relying on Rescue and Recovery to rescue or recover my system. Utter rubbish!
Thankfully, Windows Backup did the job perfectly and the only thing I lost was the weekend!