Steps to reproduce:
1. Download the attached project
2. Unzip Scripts/ch.sycoforge.Decal.zip
3. Open the included dll in a dll inspector(dotPeek)
4. Notice only a reference to mscorlib 2.0
5. Open the project in 5.6 and upgrade the API
6. Inspect the dll again

Expected result: same result, since 5.6 should not include the framework
Actual result: a reference to 4.0 is included

Reproduced on 5.6.0p2 5.6.1p3, 2017.1.0b8(as it should)
Not reproduced on 5.5(as it shouldn't), 5.6.0p1
Regression introduced in 5.6.0p2

Notes:
-API upgrade does not appear to happen if the dll was first imported into 5.5 and then the project was opened in 5.6
-Extracting while open in p2+ or opening any 5.6.p1- project in p2+ does call the API updater