Some custom SharePoint products make changes to the web.config file of a web application via SPWebConfigModification calls in order to support particular features.
Bamboo does this to support Telerik functionality with some products.
At times, some of these changes need to be modified (via additions to the web.config), or partially removed for particular Web applications in order to support functionality with other third party changes to the web.config file.
However, it is neither recommended nor a best practice to manually remove the text in the web.config file, because the web.config updates would not match what has been set in the configuration database and will likely be overwritten when you install updates or service packs for SharePoint.
Use PowerShell to remove or add web.config modifications so that changes are updated in the configuration database as well as on the server(s).
For more information, please see the MSDN article: Working with Web.config Files