There is currently no way to do this using the Hyperlapse GUI. However, you can do it by editing the Hyperlapse project file.
Hyperlapse project files (.hyp files) are zip archives that contain other files. If you rename the .hyp file to .zip, then you can extract the contents of the archive. One of the extracted files is "ProjectInfo.dat,"
which is an xml file with various fields. To re-link your video to the project, you should edit the <InputFileName> field (say, using Notepad) to point to the new location of your video file. When you're done, you'll need
to rezip the files and rename the archive back to .hyp.