Instanced prefab data still is pretty buggy. It doesn't save them 50% of the time. One scenario that I can replicate each time is:
-Edit the tilemap, paint a prefab tile, commit
-Select the prefab, change some values
-Edit the tilemap again, create a color channel
-Paint anything with the color channel
-Delete the color channel
-Commit the tilemap
Prefab instance data is no longer saved and reverted to the default values.