If you've found a new map that you'd like to add to an ongoing playthrough please follow the following steps:

1. Subscribe to new map mod(s).
2. Enable the new map mod(s) on an existing save (Save A).
3. Create a new game with the same map mod(s) enabled (Save B).
4. Quit back to main menu.
5. Find Save B's files (usually located in C:\Users\USERNAME\Zomboid\Saves) and copy and replace 'map_ver.bin' to Save A's file location (backup original).
6. Load Save A.
7. ???
8. Profit.

Removing maps or clearing an area where you'd like to add a map (in the case you've already traveled to the area before adding the map) can be done similarly, however every cell ('map_XXX_YYY' and chunkdata_XX_YY) associated with that map mod needs to also be deleted (which can be quite an arduous task to figure out exactly which those are). I recommend using the PZ Map website to help identify the coordinates if you choose to undertake this task (https://map.projectzomboid.com/).

Also, you can update the games settings mid-save by following the same process for the map_sand.bin file.