Hi Tomas,
It sounds like you might have AVCHD media and you updated your project. It is not a good idea to update your project mid-stream (however, it should not create such a big problem like this). If you do that, please make sure you have a duplicate of your project file before proceeding.
What has worked for others is to rename your media folder, then relink the footage in the new location. See if that works for you.
Thanks,
Kevin