thank you for the tip. I have changed all interfaces now and it looks good at the moment.

Here is the script I used for changing the interfaces:

from org.netxms.client.objects import GenericObject, Node, Interface, AbstractObject

# START CONFIG
###############################################################################

rootID = 108 #objects.GenericObject.SERVICEROOT # Infrastructure Services Node

##############################################################################
# END CONFIG


rootNode = s.findObjectById(rootID) # the root node object

print 'Changing items from node %s' % ( rootNode.getObjectName() )

def getSubItems(parent, depth):
    for node in parent.getChildsAsArray():
        nodeClass = node.getObjectClass()
        nodeName = node.getObjectName()

        if nodeClass == AbstractObject.OBJECT_CONTAINER:
            #print 'Checking subnode...'
            getSubItems(node, depth + 1)
        else:
            for interface in node.getAllChilds(GenericObject.OBJECT_INTERFACE): # 3 == interface
                name = interface.getObjectName()
                if name.startswith('unknown'):
                    data = NXCObjectModificationData(interface.getObjectId())
                    #data.setExpectedState(2) # 2 := ignore interface state
                    newFlags = interface.getFlags() | Interface.IF_EXCLUDE_FROM_TOPOLOGY # set exclude flag
                    data.setObjectFlags(newFlags)
                    session.modifyObject(data)
                    print 'Changed interface of %s' % (nodeName)
                    #session.applyTemplate(4754, node.getObjectId()) # add node to new template
                    #print 'Added node to new polling template'

# main
getSubItems(rootNode, 1)

print 'Done changing interfaces!'

I have a similar case and stopped this warnings at "Propoerties - Polling" of the interface with activating "Exclude this interface from network topology".

Bye
Heimo