Drawbacks of customise Sharepoint Alert Email Template in sharepoint 2010

i changed the Pre-defined Alert Template file from this location: %ProgramFiles%\Common Files\Microsoft Shared\web server extensions\14\TEMPLATE\XML\AlertTemplates.xml
How to avoid this new changes to the other sites?
Will it impact all the webapplication?

This is a default template used by all web application and you cannot restrict other web application from using it
Actually you can create your own template and use it for specific web application as per below:
http://community.bamboosolutions.com/blogs/bambooteamblog/archive/2012/08/21/how-to-customize-the-discussion-board-plus-email-alerts-for-sharepoint-2010.aspx
http://jimecox.wordpress.com/2012/01/29/modifying-the-appearance-and-email-body-of-alerts/

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    Please remember to mark the replies as answers if they help and unmark them if they provide no help. If you have feedback for TechNet Subscriber Support,
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    Dear Support,
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