No they won't, usually when u sync your Gmail account on ur phone or tablet, it installs all the softwares again. But not the data associated with those softwares. For that you need to backup the software data as well and restore it, once all softwares are installed, on your tablet with new Android.
And remember. Nexus devices are very hard to brick. So go ahead and install, customize, hack into the firmware no problems. Just read over at xda developers regarding your tablet and follow step by step on guides and would will be good to go.