Edit gps recorded track
Interesting question. I don't know if there is a better way but I can offer a couple of suggestions.

There's a thread over on BikeRadar where someone is wanting to stitch two FIT files together, there's a suggestion to convert to TCX then manually merge the files using a text editor.

http://training.bikeradar.com/forum/longest-day-road-challenge-324/combining-separate-garmin-files-into-single-ride-152481

The posts within the thread indicate that the suggested method works.

Your case is obviously more complicated since you only have the one FIT file to start with. 

So, you can manually create an activity to represent the last chunk of your ride. Garmin Connect supports this, although I don't know how functional it is. I do know that Garmin Connect will allow you to export your activity as a TCX, as I have done this. I can also suggest the site rideWithGPS, which is my preferred portal. RWGPS will allow you to manually create an activity (including drawing the route on a Google map, let you to enter start/total times, and then export it (as TCX History).

You need to register with RWGPS but I don't think you need the pay account to do anything I've suggested.

Whichever way you choose, by the end of this process you should have two TCX files that you can merge.

In passing, GPSies.com is a great site for format-to-format conversions, although in your case you'll get your resulting TCX into Garmin Connect no problem.

One thing I would ask is that you let us know how you get on - I've never needed to do this but I'm a big Garmin user and there may come a day when I'll want to know this myself

Good luck!