I used this http://www.showeq.net/forums/showthread.php?6098-SOE-or-Mapfiend-to-SEQ-map-conversion-script to convert after I ran the merge script. Took a lot longer than it did when I ran mapconvert on original unmerged map files.
I was just at new Chardock (EoK expansion) map showed perfectly there.
Also Palatial Guild Hall map would not load because showeq called for guildhalllrg_int.map. There isn't any map files but there is guildhalllrg.map and I "cp guildhalllrg.map guildhalllrg_int.map" and it shows up fine. .... Not like you'd need a map for that zone