The "Pipe Through" filter action does not pipe the email to the external program, not even on manual filtering. It is ofc intermittent and hard to reproduce reliably. 

I have the following script for running crm114

#!/bin/bash
TIME=$(date +"%d/%m/%Y %H:%M:%S")                                                                                               
LOG=~/logs/crmlog                                                                                                               
mkdir ~/logs &>/dev/null                                                                                                        
touch $LOG                                                                                                                      
echo $TIME >>$LOG
cp /dev/null ~/logs/copy                                                                                                               
exec crm -u $HOME/.crm114 mailreaver.crm | tee ~/logs/copy 2>> $LOG

This will enter a time stamp in the log file and copy any data from the pipe into the "copy" file.

When Kmail starts failing the filtering, the logs shows that the action was run, but the "copy" file only contains the crm114 header message indicating that the pipe was empty.

there seems to be 3 workarounds none that work reliably all the time..
1. remake the filter rule, its enough to edit the rule and resave.

2. stop and start akonadi, making sure the filter agent is restarted.

3. log out from the kde session or reboot

One would think that rebooting would fix it, but have had cases where the filtering fails on a fresh reboot / login first time kmail session, where resaving the rule fixed it...