Hi, I confirm the issue when upgrading from debian wheezy (kdepim 4.4.11.1) to 
jessie (kdepim 4.14.1)

I suggested this workaround on https://bugs.kde.org/show_bug.cgi?id=326474

During migration :
The filters are migrated but kept in file ~/.kde/share/config/kmail2rc
Thus, they are applied to the emails, but not viewable in the filter 
configuration windows of kmail2

My workaround to migrate the filters :
1. Copy all [Filter #xx] sections from ~/.kde/share/config/kmail2rc to 
~/.kde/share/config/akonadi_mailfilter_agentrc

2. In the latter add this section and in the filters value specify the count of 
Filter sections you added (instead of yy)
[General]
filters=yy

3. Remove the [Filter #xx] sections from ~/.kde/share/config/kmail2rc


KR


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