Hi Matt,
your actual setup sounds very reasonable for what you want to do.
About the chance of filtering out some traffic, in your case ICMP
datagrams, you can use Pre-Tagging. 

1. create a new Pre-Tagging file (if you are not already using
one for other purposes), say pretag.map; insert into it a line
like the following:

id=100 ip=<NetFlow agent IP address> filter='ip proto 1'

The above line associates the tag '100' to each packet matching
the filter 'ip proto 1' (ie. all ICMP packets) coming from your
NetFlow agent (in your case, it's the Packeteer Packetshaper).

2. link your Pre-Tagging file into your nfacctd configuration:

pre_tag_map: /path/to/pretag.map

3. attach a negative Pre-Tagging filter - matching tag 100 - in
your nfacctd configuration:

pre_tag_filter[sql_instance_a]: !100
pre_tag_filter[sql_instance_b]: !100

To be even more correct, because one of the two instances should
be accounting incoming traffic, you can stick the filter only to
that. 

Cheers,
Paolo

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