Development for this tool has been continued in here. I wasn't able to easily upgrade the legacy VB code so I decided to rewrite the tool in Go.
A tool to create, delete, and edit maps on a Minecraft world, and easily convert images to map art.
Minecraft stores maps in the data directory of each Minecraft save. Each map is stored as an NBT file with the name map_[id].dat. The idcounts.dat file keeps a record of the latest map ID.
Each colour is stored in the map file statically; it does not get calculated everytime from the actual blocks. Hence the reason why you need to reload the chunks to update a map.
Because of this, map art can be stored as colours in the map file, without the actual terrain needing to exist. Minecraft Map Manager simply converts an image into a limited colour palette with some algorithms, and writes this data to a map file.
Since Minecraft Snapshot 19w02a (1.14), maps can be locked, meaning there is no risk of the map being overwritten if the chunks are reloaded.