Try to recreate material libraries to fix the disconnecting shaders issue.

MatLibFix.py

from win32com.client import constants as c
xsi = Application
log = xsi.LogMessage


def XSILoadPlugin(reg):
	reg.Author = "pboucher"
	reg.Name = "MatLibFix"
	reg.Major = 1
	reg.Minor = 0

	reg.RegisterCommand("MatLibFixStep1","MatLibFixStep1")
	reg.RegisterCommand("MatLibFixStep2","MatLibFixStep2")
	#RegistrationInsertionPoint - do not remove this line

	return True


def MatLibFixStep1_Init(ctxt):
	cmd = ctxt.Source
	cmd.Description = "Pre save step of the 2011 MatLib fix problem"
	cmd.SetFlag(c.siCannotBeUsedInBatch, True)
	cmd.SetFlag(c.siNoLogging, True)
	cmd.ReturnValue = True

	return True


def MatLibFixStep1_Execute():
	msg = 'After processing mat libs and saving scene, this will quit Softimage.'
	flags = c.siMsgOkCancel | c.siMsgExclamation
	if XSIUIToolkit.MsgBox(msg, flags, 'Process and Quit?') == c.siMsgCancel:
		return True
		
	for matLib in xsi.ActiveProject.ActiveScene.MaterialLibraries:
		matLib.Parameters('storage').Value = 2
		matLib.Parameters('filename').Value = 'MatLibs\\' + xsi.ActiveProject.ActiveScene.Name + '__' + matLib.Name + '.xsi'
		path = XSIUtils.ResolvePath(matLib.Parameters('filename').Value)
		xsi.ExportMaterialLibrary(path, matLib, "")
	xsi.SaveSceneAs()
	xsi.Quit()
	return True


def MatLibFixStep2_Init(ctxt):
	cmd = ctxt.Source
	cmd.Description = "Post save step of the 2011 MatLib fix problem"
	cmd.SetFlag(c.siCannotBeUsedInBatch, True)
	cmd.SetFlag(c.siNoLogging, True)
	cmd.ReturnValue = True

	return True


def MatLibFixStep2_Execute():
	for matLib in xsi.ActiveProject.ActiveScene.MaterialLibraries:
		if matLib.LockLevel != c.siLockLevelNone:
			matLib.UnSetLock()
		matLib.Parameters('storage').Value = 0
	xsi.SaveSceneAs()
	return True