I don't use the ThorUI myself .. but if you just want the original (default UI) pet window then you should be able to go into the folder where the ThorUI is installed (C:\EQ2\UI\ThorUI)? and delete the file called "eq2ui_mainhud_pet.xml".
If it's an alternative version of the ThorUI pet window you want then all I can think of is to uninstall the ThorUI ... make sure the ThorUI folder has been removed from the C:\EQ2\UI folder ... re-install ThorUI with the settings you want.
It sounds like it's not un-installing correctly or leaving some files behind ... re-installing EQ2 wouldn't affect the ThorUI files apart from changing the EQ2.ini file which sets which UI you use.
Hope that's of some help