I don't really understand what that line does, I modified you publish() function and took out the json vars and MQTT lines and left everything else including setFilterBypass.

My getOrientation():
Private Function getOrientation(type As Integer) As ListOfByte
        accel.SetFilterBypass(True) 'enable HP filter bypass (so that values read below do not go through HP filter) - this is the normal configuration
        accel.GetAccel() 'dummy read
        Do
            Thread.Sleep((accel.GetmsFromDataRate* 1000).ToInteger) 'wait 1 clock cycle for new unfiltered reading
        While Not accel.NewDataAvailable() 'wait for new data
        Dim accelValues As ListOfFloat = accel.GetAccel()
        Dim PitchRoll As ListOfFloat = accel.GetPitchRollDegrees()
        accel.SetFilterBypass(False) 'disable filter bypass again, this means the *values* given by interrupts (if you are displaying them) will be with HP filter enabled.
       
        Dim msgData As ListOfByte = New ListOfByte()
        msgData.Add(0x08) '08 is an indication to Losant that this payload contains location data
        msgData.AddInteger(type)
        'msgData.AddFloat(accelValues(0)) //x
        msgData.AddFloat(accelValues(type)) //y
        'msgData.AddFloat(accelValues(2)) //z
        'msgData.AddFloat(PitchRoll(0))
        'msgData.AddFloat(PitchRoll(1))
       
        Return msgData         
       
    End Function
Your publish() from End Motion program -> https://github.com/NickWaterton/mcScript/blob/master/libraries/accelerometer/lis2dh12/examples/EndMotionTest/EndMotionTest.mcScript:
    Shared Event Publish() RaiseEvent Every 10 Seconds
        accel.SetFilterBypass(True) 'enable HP filter bypass (so that values read below do not go through HP filter) - this is the normal configuration
        accel.GetAccel() 'dummy read
        Do
            Thread.Sleep((accel.GetmsFromDataRate* 1000).ToInteger) 'wait 1 clock cycle for new unfiltered reading
        While Not accel.NewDataAvailable() 'wait for new data
        Dim accelValues As ListOfFloat = accel.GetAccel()
        Dim PitchRoll As ListOfFloat = accel.GetPitchRollDegrees()
        accel.SetFilterBypass(False) 'disable filter bypass again, this means the *values* given by interrupts (if you are displaying them) will be with HP filter enabled.
        Dim jint As Json = New Json
        'NOTE: If you put too much in a json object, it will cause a run time error (overlow) and the module will reboot
        '      Below is too much for one json object, so I've split it into two
       
        Dim jData As Json = New Json
        jData.Add("X_Accel", accelValues(0))
        jData.Add("Y_Accel", accelValues(1))
        jData.Add("Z_Accel", accelValues(2))
        jData.Add("Pitch", PitchRoll(0))
        jData.Add("Roll", PitchRoll(1))
        'jData.Add("PitchAlt", PitchRoll(2))
        'jData.Add("RollAlt", PitchRoll(3))
        If Start_Motion_Detected Then
            jData.Add("State", "Moving")
        Else
            jData.Add("State", "Stationary")
        End If
        MQTT.Publish("Data", jData)
       
        If pin1data.Count() > 0 Then
            jint.Add("Pin1 Count", pin1count) 'number of interrupts generated
            jint.Add("Pin1", pin1data)
        End If
        If pin2data.Count() > 0 Then
            jint.Add("Pin2 Count", pin2count) 'number of interrupts generated
            jint.Add("Pin2", pin2data)
        End If
        If jint.Count> 0 Then
            MQTT.Publish("Ints", jint)
        End If
       
        pin1data.Clear()
        pin2data.Clear()
        pin1count = 0
        pin2count = 0
    End Event
Should I leave it as true?