The best thing I can recommend is keeping the maps in the map maker, which are also displayed in Cape of Distant Worlds. Mainly because you will regret it if you want to go back and change anything. What I can suggest however, is packing a download of and for the map (with all the .fhm's, .fho's and .fhs's or .fhw's if you've used any). Then you have that out of the way and you can delete the 'copy' of the map in Cape of Distant Worlds.
Deleting your map 'copy'.
To delete the map 'copy' (referring to the exported map portal), you just need to remove the .fhm file from your Local Disk (C:) \\ Feral Heart \\ Exports folder. As shown in the example below with my Gawana Island Map. Once deleted, just relaunch Feral Heart and the map will be removed from Cape of Distant Worlds.
(http://i.imgur.com/14TTrsm.png)
Deleting a map from Map Maker.
Of course, this is your choice, whether you choose to keep the map in map maker and save everything for possible future modifications or not. However, if you are wanting to remove maps from the map maker, you just need to remove the map's folder, as well as the .map file. If I remember correctly, the .map file is what allows the map to be listed in the Map Maker. I will share an example of what I'd remove if I were to remove my Gawana Island Map from the Map Maker.
(http://i.imgur.com/iyHalrY.png)
And because I'm a total clean freak, here is what I'd remove to keep my folder clean. Unless you'd like to re-use the height or terrain map of course. The following highlighted contents are my Gawana Island Map's height and terrain masks, as well as the Photoshop documents I saved in there in order to make the height and terrain maps.
(http://i.imgur.com/XOZawO6.png)
What you decide to do is all up to you in the end of course. However, I'm completely grateful that I didn't remove the map from the Map Maker just to keep the exported map instead. Now I can modify whatever I want and it's currently having a few re-models in areas of the maps ready for public download.
Hopefully these are the answers you were looking for. Best of luck to you on getting this issue sorted.