If you are trying to remove an entire section from the config file rather than individual keys, you have to use the "clear" tag rather than "delete". If you switch your config to "<excludes> clear", you should be able to skip all of the individual exclude entries from the CFX file.
Here is a brief example to illustrate the difference between the tags...
Config before:
<setup>
loglevel = 0
</setup>
<profiles>
<server1>
active = yes
ip = 192.168.0.11
</server1>
<server2>
active = yes
ip = 192.168.0.12
</server2>
<server3>
active = yes
ip = 192.168.0.13
</server3>
<server4>
active = yes
ip = 192.168.0.14
</server4>
</profiles>
CFX file:
<profiles>
<server1> delete
</server1>
<server2> delete
ip =
</server2>
<server3> clear
</server3>
</profiles>
Config after applying CFX file:
<setup>
loglevel = 0
</setup>
<profiles>
<server1>
active = yes
ip = 192.168.0.11
</server1>
<server2>
active = yes
</server2>
<server4>
active = yes
ip = 192.168.0.14
</server4>
</profiles>