arcpy.SpatialJoin_analysis() not overwriting existing featureclass, not returning all features

Question

I'm calling a python script from a custom very high level macro language script. Within the python script there is an arcpy.SpatialJoin_analysis() command. For some reason if the output from this operation is not in the workspace geodatabase already (meaning I deleted the previous output prior to running the script), the spatial join runs but only returns 20 records out of 259. If I run it a second time, it fails to execute due to a schema lock (error 000464). I can't get the error message because the python window disappears too quickly. If I run it from the ArcMap python command window no error message comes through. I have the script set to overwrite output and my geoprocessing options allow for overwriting previous geoprocesses.

import arcpy

print" Running Python Script"

# Set up workspace and mxd
workSpace = r"C:\RS_Data\Workspace\BATCH_CO_161_imports\gisdb\layers.gdb"
arcpy.env.workspace = workSpace
arcpy.env.overwriteOutput = True

try:

    # Perform a spatial join so the new routes can be assigned to the service location layer

    target = r"C:\RS_Data\Workspace\BATCH_CO_161_imports\gisdb\layers.gdb\Service_Location"

    join = r"C:\RS_Data\Workspace\BATCH_CO_161_imports\gisdb\layers.gdb\Suburban_Rec"

    outFC = "XX_Recycle_SPJ"

    arcpy.SpatialJoin_analysis(target, join, outFC)

    arcpy.MakeFeatureLayer_management(outFC,"layerFC")

    # Select all records in layerFC

    arcpy.SelectLayerByAttribute_management("layerFC","NEW_SELECTION")


    # Remove relevant commodity codes so they do not get deleted

    QF1 = '\"Product_Code\"'
    RV1 = '( \'R10R\', \'R10RBP\', \'R20R\', \'R20RBP\', \'R32R\', \'R32RBP\', \'R64R\', \'R64RBP\', \'R96R\', \'R96RBP\', \'R10RBY\', \'R20RBY\', \'R32RBY\', \'R64RBY\', \'R96RBY\', \'R10REC\', \'R20REC\', \'R32REC\', \'R64REC\', \'R96REC\')'
    WC1 = QF1 + ' IN ' + RV1

       arcpy.SelectLayerByAttribute_management("layerFC","REMOVE_FROM_SELECTION", WC1)

    # Add unmatched records back to selection

    QF2 = "Status"
    RV2 = "M"
    WC2 = """ {} <> '{}'""".format(QF2, RV2)

    arcpy.SelectLayerByAttribute_management("layerFC","ADD_TO_SELECTION",WC2)

    # Add records with incorrect service day back to selection

    QF3 = "ServDay"
    QF4 = "Service_Day"
    WC3 = """ {} <> {} """.format(QF3, QF4)

    arcpy.SelectLayerByAttribute_management("layerFC","ADD_TO_SELECTION",WC3)


    QF5 = "Week"
    QF6 = "Wk"
    RV3 = ""
    WC4 = """{0} <> {1} AND {1} <> '' """.format(QF5,QF6) 

    arcpy.SelectLayerByAttribute_management("layerFC","ADD_TO_SELECTION",WC4)

    arcpy.DeleteFeatures_management("layerFC")

    # Bring over route values rom spatial join

    with arcpy.da.UpdateCursor("layerFC",["OfficRT","Route"]) as cursor:
        for row in cursor:
            row[1] = row[0]
            cursor.updateRow(row)

    # Bring over sequence values from Tower ODBC table
    SeqTable = 'S:\\Shared\\RouteSmart\\CO_161_Cleanscapes\\From_Tower\\CLS_XX_Last28Days.xlsx'

    arcpy.ExcelToTable_conversion(SeqTable,"Join_Table")

    QF7 = "SVCCODE"
    QV3 = "R%R%"
    WC5 = """ {} LIKE '{}' """.format(QF7, QV3)

    arcpy.MakeTableView_management("Join_Table", "RecSeq", WC5)

    with arcpy.da.UpdateCursor("RecSeq", "CUSTID") as cursor:
        for row in cursor:
            row[0] = str(row[0]) + "001"
            cursor.updateRow(row)
    print "UPDATED ROWS"

    joinFc = "RecSeq"
    joinIdFld = "CUSTID"
    joinValFld = "OLDSEQUENCE"

    valueDi = {x[0]: x[1] for x in arcpy.da.SearchCursor(joinFc, [joinIdFld, joinValFld])}

    with arcpy.da.UpdateCursor("layerFC", ["Sequence", "Address_ID"]) as cursor:
        for update, key in cursor:
            if not key in valueDi:
                continue
            row = (valueDi[key], key)
            cursor.updateRow(row)
    del cursor

    # Export final feature class to output workspace
    outputWS = r"C:\RS_Data\Workspace\BATCH_CO_161_Recycle_export\gisdb\layers.gdb"

    finalFC = r"C:\RS_Data\Workspace\BATCH_CO_161_Recycle_export\gisdb\layers.gdb\XX_Recycle"
    arcpy.FeatureClassToFeatureClass_conversion("layerFC", outputWS, "XX_Recycle")

except arcpy.ExecuteError:
    print(arcpy.GetMessages(2))

    # Delete temp files
finally:
    arcpy.Delete_management("layerFC")
    arcpy.Delete_management("RecSeq")

Answer 1

After further research I discovered that deleting rows from a layer file using arcpy.DeleteFeatures_management() will also delete records from the parent featureclass simultaneously. This is why the SPJ output only has 20 features left in it. I thought that once I made a layer file (layerFC) the DeleteFeatures_management would only touch those features.