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Good Afternoon Barnes Financial Group, 

Typically when support is helping you to delete any registry keys, we are deleting keys either in the EasyACCT folder or the pendingfilerenameoperations key in Session Manager. Are these the keys you are referring to? Both would affect the EasyACCT program or the install respectively. Neither of these keys have any impact on your Windows user profile or any Windows settings and likely not the cause for any Windows issues. 

Also, before making a change in the registry, we usually walk you through saving a backup of your registry, do you know if this was done? You may be able to restore the backup of your registry to confirm if he impact was due to deleting these keys. 

Thank you for your post in the Accountants Community!