Preventing eclipse from deleting files in web folders deployed under tomcat when sync -

we using eclipse develop web projects. have tomcat server defined in servers pane. inside there 2 web modules deployed:

tomcat:
* module1
* module2

after initial sync place files inside module folders manually. example: c:\tomcat\webapps\module1\main.swf

it seems when making changes , eclipse resyncs main.swf deleted folder.

is there way prevent this?