The short answer: In a nutshell, EQ2MAP should only be providing maps that aren't normally supplied by the game. It should not be resetting fog for any zones you normally see a map for.
The long answer:
Each zone that actually has a map, has an associated Zone Rectangle (ZoneRect) used for various calculations, including what areas of that map have been revealed if fog is present for that zone.
If the ZoneRect is changed, EQ2 tosses all fog reveal data and starts that zone's fog reveal from scratch. Reverting back to a default ZoneRect again refreshes the fog reveal. It DOES NOT restore previously revealed areas.
Fog reveal data is either stored on the server or inside an encrypted file we can't edit.
With that said, the EQ2MAP team has tried not to replace maps already suplied with the standard install or sent down by the server, essentially any zone you'd already see a map for. Off the top of my head, this includes all city zones, Antonica, Commonlands, EL, Nektulos, Thundering Steppes and Zek.
This actually limits what we can do with the Map Window, but was deamed least intrusive to users.
Its possible some obscure zones, for which the server provides maps, have been replaced by EQ2MAP that I'm not aware of, but I doubt it.
Its also possible that at some point the EQ2MAP team may need to correct a flawed ZoneRect for an area they do provide a map for. This would only happen if the ZoneRect is seriously flawed. Everyone on the team understands the frustration caused by refreshing fog and will avoid doing this unless absolutely required.
Some map related mods, such as my MiniMap external window, make use of "supplimental" maps sent down by EQ2MAP (as a courtesty to other modders) that aren't used by the main map window. You'll see map files for the above mentioned zones, but rest assured they aren't used by EQ2MAP and aren't interfering with your fog