You might want to make a backup before trying this, but...
The best way to avoid any problems of this sort is to actually go to Object Maker, load up the objects you are using one by one, and save them to their own object group. I usually just save them under a group with the same name as the map, and then the "-Objects" suffix. Ex: if the map was Temple -> TempleObjects
It's easier if you leave all the actual Object Names the same.
Now, you can go through media>terrains>Temple (or whatever your map is actually named) and open TempleObjects.cfg (or again, whatever your map is actually named, "-Objects.cfg").
Inside is a list of all placed objects and their location, and each section is headed with the syntax of
[ObjectGroup/ObjectName]
Use Ctrl + H (or go to Edit... -> Replace)
Replace the old Object Group name(s) with your new one.
Save that, relaunch the game, load up the map, and export it then.
With everything in it's own group, you might have more luck.