Yes this is a horrible glitch in the Evernote software. When you have an item selected if you drag another item into the PC Suite it will overwrite the original item with no way to get it back ever. Undo does not work. This issue is a very sloppy programming issue in my perspective this along with many other issues like the very glitchy table system in Evernote make the software almost unusable because your data is not safe.
The way I achieve unlimited stacks is by using X-marks in conjunction with Evernote. Every time I add a note to Evernote I just grab the note URL then create the folder structure the way I want it in X-marks with the URL. Not only does this breaks me out of the limitation of Evernote stacks but I get all the benefits of X-marks too! I am sure sooner or later someone will create a third party application that does something like this automatically because everyone loves Evernote's storage model however there has to be a massive market for people who want to break these stack limitations. I would pay like a $100 bucks any day to have a software that would break me free of tagging. Personally it doesn't appeal to me because it's not visual like folders. For the time being Evernote is the 100 pound gorilla in the room and it's benefits still outweigh it's shortcomings.