Can't reinstall .net framework 2.0

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Customer came in not being able to open her NeatWorks Scanner software. Hard drive was bad so used dd to clone to new one. After clone ran chkdsk and sfc. When I open the Neat program is says it has Stopped Working and the fault module name is mscorwrks.dll, which has to do with .net. Looking at the event log it is specifically with the installed .Net Framework 2.0.50727. This is Windows 7 64bit. It has .Net 4.0 and 3.5 successfully installed and functional. I can't figure out how to uninstall and reinstall .Net 2.0. The steps I have taken were disabling 3.5 (thinking it'd get 2.0 too), using .NET Framework Cleanup Tool (which doesn't have 2.0 listed), and Microsoft's .Net Repair utility. When I try to install .Net 2.0 from the 64 bit installer it says that it is already on my system and when trying to install 3.5, which includes the previous .net versions, nothing happens. Your help is appreciated!
 
I've managed to get it uninstalled via this knowledgebase, but now when I run the 2.0 installer it says that it is a part of the operating system and can't be installed. Right now running sfc again.
 
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