When you uninstall Fences version 1.x, you will get TWO prompts. One of them will ask if you want to delete the current settings, choose NO. This way you get to keep the Fences you had.
If you choose Yes, it will lose the settings and fences.
EDIT: By the way, since you did not lose anything yet, a better thread title would be "Will I lose my icons?" OR maybe "Icons loss question".