Upgrade to Flex 3.5 - removes html templates files

I came across the problem when I upgraded my Eclipse Flex Builder Plugin to use Flex 3.5 SDK.

When I was using clean my project option, it was removing html-template folders content, and solution is (I found a solution on web from one blog/ article):

Go to your project's properties (right click, Properties)
Go to Flex Compiler
Under "Html wrapper" un-check "Generate HTML wrapper file" Click "Apply"
Then check "Generate HTML wrapper file" (the same one you just unchecked)
Click "Apply"
You should now see that the html wrapper files are regenerated.

This happened to me when I used the clean option on one of my projects.