As you have experienced, Wine is a work in progress with certain applications and functionality.
The clean uninstall functionality your looking for is not fully realized in Wine (and Windows for that matter but that's a different topic for a different post) so you have to "engineer" it.
What I recommend that you do is virutalize Ubuntu (I use VirtualBox) and install the Wine package in a Ubuntu virtual machine, then save a copy of the state of the VM (snapshotting, fully VM copy, etc.). Whenever you encounter a misbehaving Wine application that interferes with your other Wine applications just trash the VM and fire up your snapshot. Wa'la! You just engineered a clean uninstall without wasting time debugging it, nor trashing your .wine folder and having to reinstall all the other programs!
Unless your a Wine/Windows developer, your going to chase down the rabbit hole trying to find a "solution" to your problem which ultimately, most likely entails developing/improving Wine code.
if you are feel free!!!! But, as you noted your a novice so... hope that helps!




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