I installed the update from 2.5 to 2.6. I put it in a different folder. All files for 2.5 are still there. You should have removed the old regardless of folder shouldn't you.
No, the files should not have been removed. The reason you changed the folder might have been because you did not want to overwrite the old installation. A pop-up (or something) asking if you wish to remove the old installation would have been convenient, though.