When I check the configuration I see that the EPG source list is completely blank and I will have to set each one again.
Seems strange and more of a tvheadend issue than a zap2xml problem. Next time it comes up blank, check and see what the update time is on the xmltv.xml file. That way you can narrow down if there is an issue with the file being generated - or of there is an issue with tvheadend holding your configuration. It would also help to post your hardware setup.
There has been an issue that I've read about with the epg in kodi going blank - but you mention that the epg in tvh is blank and that the epg source fields have gone blank as well. That I have not seen - but may be worth posting in the tvheadend forum.