How to reproduce:
1. Open user-submitted project (TMPDirty) and open the SampleScene
2. Select the TextMeshPro GameObject and find the 'Sorting Layer' setting in 'Text Mesh Pro (Script)' Component
3. Change the 'Sorting Layer' setting and the 'Order In Layer' value
4. Save the Scene, switch to New Scene and back to Sample Scene

Expected result: 'Sorting Layer' and 'Order in Layer' values were saved
Actual result: 'Sorting Layer' and 'Order in Layer' values were not saved

Reproducible with: 2018.1.9f2, 2018.2.7f1, 2018.3.0a11

Notes:
The issue appears in all TMP package versions
A temporary workaround is to dirty the scene some other way, for instance, creating and deleting a GameObject