when relinking there is no need to delete any files. UMDGen will automatically reduce the iso size correctly.
Here are the basic steps on relinking:
1. Open your untouched ISO in UMDGen.
2. Open UMDGen to the correct folder that contains the movie files.
3. Right-click a movie that you want to KEEP and relink all others too (a short movie is best)
4. Select from the dropdown Menu 'File Relinker -> Use Selected File As Source'
5. Select all the movie files you wish to be relinked.
6. Right-click and select "File Relinker -> Relink To Source'
Now all selected files will be relinked to the source file (look at the LBA positions - they are now all the same). You will also notice ISO size has been reduced.