Solving this issue is as simple as changing the referenced files to managed files. You can do this in Aperture, by selecting the offending videos in your Aperture library, then:
- From the Aperture menu bar, select File > Consolidate Masters.
- In the dialogue box, choose whether you would like to copy the referenced files to your master library location (this keeps a copy of the file in both locations), or if you would like to move the file to the managed library location. Once the video is in the managed location, you will be able to access it in iMovie.
Keep in mind that when moving or copying referenced files you need to have enough space on the drive that contains your referenced library.