Recent Subversion 1.4 clients write meta data (files in the .svn subdirectories) in the new format. IntelliJ IDEA versions before 6.0.2 are not compatible with this format.

If you update/checkout your project using SVN 1.4 or Tortoise SVN or other SVN client that already uses the new format introduced in the Subversion 1.4 release, then IntelliJ IDEA will lose file tracking and will report that your files are not under the SVN control.

The solution is to rollback your client to pre-1.4 version (1.3.5, for instance) and perform clean project checkout (clean means that you need to delete your files and make a checkout into the empty directory). Another option is to checkout from IntelliJ IDEA (File | Check out from version control | SVN) and do not use 1.4 SVN clients with the same project.

Full Subversion 1.4 support is available since IntelliJ IDEA 6.0.2 release.