pc1 - Win10
Manually rename BoardManager in Project window
Manually rename MonoBehaviour class
Manually rename ref in GameManager
Save project
NOTE: Collab Toolbar sees BoardManager_RENAME.cs as a Move
NOTE: Collab Toolbar sees GameManager.cs as Modified

pc2 - OSX 10.11.6
Manually edit BoardManager to include method Update() text
Manually edit GameManager to remove excess lines/whitespace
Save project
NOTE: Colalb Toolbar sees BoardManager.cs and GameManager.cs as Modified

*********************************************************************************************
GUID CHECK:
pc1
GM.cs = guid: 5b391fbc4e12a499b9aaf9f088dbd95b
BM_RENAME.cs = guid: 585ca15f7b13a49d5bfb9dc19f1b5981

pc2
GM.cs = guid: 5b391fbc4e12a499b9aaf9f088dbd95b
BM.cs = guid: 585ca15f7b13a49d5bfb9dc19f1b5981
*********************************************************************************************
Publish from pc1
Update on pc2

pc2:
Merge Conflict on BoardManager.
Console error: BoardManager_RENAME could not be found Are you missing an assembly reference?

pc2:
Launch external tool.
Correctly merge both files to include the rename and the new code in Update()
Save Merge (Apple FileMerge)
Close FileMerge

pc2:
Console error is resolved
Select Collab Toolbar and see changes to Publish
NOTE: Collab Toolbar sees GameManager.cs as Modified
NOTE: Collab Toolbar sees BoardManager.cs as Modified
NOTE: Project window still show Assets/BoardManager.cs and *****NOT BoardManager_RENAME.cs*****

Repro'd with 5.5f3