Desktop behaving oddly, new shortcuts appearing in $HOME directory instead of Desktop folder

So I installed WineZGui looking for a maybe faster alternative to winetricks and found I preferred winetricks so went ahead and uninstalled it. Made from src and removed it from src and since then choosing either Desktop view or Folder view from Configure Desktop Settings will no longer restore the default behaviour of game desktop files being created on the desktop and also the .desktop extension is being displayed on the old entries I restored from a Desktop folder backup. This isn’t to big of a deal but a few other things a behaving oddly and generally making a confusing mess which will I guess only get worse.
I have an another user setup just in case and that somehow was affected as well so I deleted that other user and created a totally new user without problem.
A bunch of folders were renamed to all lower case and all spaces were replaced with underscores breaking most of the wine folders but I have since restored those (hopefully).
In the Configure Desktop Settings you can point to a specific folder if you want to represent your desktop but the game and program entries are still created in $HOME.
How would I restore the desktop to it’s former glory?
Making another user is an option but I’m afraid if I copy over the ~/.local and ~/.config folders to try and save all my program and desktop settings that it will just inherit the same odd behavior.
Any pointers would be appreciated.

Edit: There is the file
which shows where the custom Desktop folder location is, under
but upon change the behavior has remained.