How to reproduce:
1. Open the attached "FontRepro5.5later" project and build it by going to File --> Build settings --> Build
2. Open the Editor.Log, scroll down to "Used assets and files from the Resources folder..." line and notice that the following fonts have been included in build: "varsity_regular", "Freshman", "college", "Quaterback Fight"
3. Inspect the "Quaterback Fight" and "varsity_regular" fonts in Project window, remove the "Freshman" and "College" fallback fonts from their respective Font Name lists
4. Save your project, exit the editor and re-open it
5. Build your project again, open the editor.log and scroll down to "Used assets and files from the Resources folder..." line

Expected result: Only "varsity_regular" and "Quaterback Fight" fonts are included in build
Actual result: All the fonts that WERE used as the fallback fonts, but have been removed from the Fonts list are still included

Reproducible with - 5.5.3p1, 5.6.0p2, 2017.1.0b1
Not reproducible with - 5.4.5p1