How did you add your custom map? Did you make a new map_cache.dat with the normal maps + your custom map or you merge the existing map_cache.dat with your custom map?
You can rename the map_cache.dat into something else like map_cache[backup].dat or something just in case anything happens. You don't really have to delete it.
What will be affected is the maps that are included in the original map_cache.dat MAY not be included inside your own compiled version of map_cache.dat, That depends on the content of your ragnarok file.
For example, the original map_cache.dat contains maps like poring_c01,poring_c02 while your ragnarok client does not have the poring_c01,poring_c02 when it compile. So those 2 maps will be missing from your version.
Advice : Merge the existing map_cache.dat with your custom map to avoid any missing maps. Unless you're inserting custom maps like custom prontera, izlude which requires to make a new map_cache.dat from start.
**Remember to recompile your server**
Hope this help. =)