This is one of those, "lets take it apart and see what we got" ordeals . :M
Sometimes these repairs become more involved as you get into it. Water damage can travel , depending how you park it during storage periods.
Before you start, make sure you have a barn or place to do this, to keep things dry for a period of time.
It gets expensive taking up time in a dealers bay, that's the alternative. I have seen them park them outside under a tarp while they wait for parts. (happened to me under warranty,waited 6 mos. outside, covered in a tarp. A one year warranty means it takes one year to get things done. If paying cash, it would have taken six days)
The dealer said its a one piece ordeal because that's the correct way to do it. They don't 'cut n patch' seams because they can be seen, its not an original look and not professional.
The other possible reason to do a one piece repair is the water will seek a low point to settle or exit. If the delamination is up high on the trailer and you repair and patch it there, you might still have water damage in the lower portion. Delamination may later occur and he would have to charge you all that labor all over again.
If the delamination is already at a low point ?
As long as you do not mind having a seam across the front of your trailer, you can cut the filon and make the repair where you need to do it. Be prepared to do some scraping to remove the old filon and glue.
You can cut a piece of new filon to cover the repair but you have to use molding to cover the seam. Pick a spot on your trailer as best you can to hide the new seam ( at least try to make it blend as best you can )
What caused the leak ?? A roof seam, a vent cover seam or a clearance light would be my guess .
Many people remove those cheap clearance lights and replace them a better light then caulk it in using Proflex RV.
I would clean and use self leveling Dicor on the roof seams and vents. Once they are fully dry (a few days) i would cover them using Eternabond tape. Add a bead of Dicor at the ends of each length of tape to prevent premature lifting.
There are youtube videos on how to do this and many rv websites where people have done it, posted the materials they used and all the 'how-to' pics.