For future reference, here's how we decided to handle MDK's entries for compound lexical suffixes (e.g. apqən, qnwil, etc.):

-keep compound lexical suffixes as their own entries in the database

-tag them with corresp in hyph - e.g.

<hyph>=<m corresp="ap-1 qin">ápqən</m> </hyph>

-add lexical-suffix-compound to their feature structures:

<fs>
<f name="baseType">
<symbol value="suffix"/>
</f>
<f name="derivational">
<symbol value="lexical-suffix-compound" />
</f>
</fs>

I added <symbol value="lexical-suffix-compound" /> to feature_system.xml after discussion with Martin and Ewa.