When you do a "Resume" action in Flash Builder, your current project is deleted. Then Flash Builder recreate the project from scratch. That's why svn files are deleted.
My workaround is to export my Catalyst compatible project (FXP) and open it directly in Flash Catalyst. When I've done, I save it and import this FXP file into a new project in Flash Builder. And I use the "merge" functionality ("compare with other project" menu or something like that). After that, I delete the new project and commit changes of my initial project on SVN.
If somebody has a better workaround, I'm interesting.
You can separate your Flex project from your Flash Catalyst components/skins.
One way of doing is to create a Flex library project (tick the checkbox for FC compatibility checking), create some custom Flex components in it in ActionScript, export that library project as a FXPL from Flash Builder and import that FXPL in FC in a blank project (from the project library). Once you are done skinning your components, export back the FXPL from FC and import it in Flash Builder. Check here:
Learn Flash Catalyst CS5.5 - Designer/Developer Workflows in Flash Catalyst and Flash Builder | Adobe TV
Learn Flash Catalyst CS5.5 - Using Custom Skinnable Components in Flash Catalyst CS5.5 | Adobe TV