I clean my register using CCleaner on all my machines, every month. I have done this to all my laptops and PCs, and others', for over four years. Never have I had any problems, and it usually speeds up the PC.
The whole point is to get rid of files that are no longer in use, and if somehow a file that's still in use gets deleted, a new one would automatically be made by the program as soon as you would run the application that it regards.
So perhaps you should look into it again, and take back your warning. 
I had some issues with the free versions of registry cleaners (like CCleaner), but a payed version works fine.
Here's a video I uploaded with me crashing, as soon as I typed in /do 24 (sit animation command) I crashed:
Packetloss