Rebuilding maps vmaps and mmaps can do absolutely nothing with visibility of map. You have done something really terribly wrong, what had nothing to do with correct server-side map extracting procedure.
To extract server-side maps, insert your DBCs into Locale folder MPQ and your custom map and model files into Data folder. If you want to really make sure by a little bit hacky way that everything really goes right, follow this:
1. Copy your WoW client, make a new one which will be just for extracting files. We will most likely make this client useless by our edits, thats why we are doing it on copy.
2. Insert all your DBCs into your last Locale patch. For enGB it would be ...WoW/Data/EnGB/Patch-enGB-3.mpq
3. If you weren't editing any blizzlike maps, skip this whole step.:
3.a. Get your edited map files. You need to have all ADTs, WDL (if any) and WDT file of whole map all together (even with some blizzlike ADTs you may have not even edited, extract such blizzlike files and merge them with your edited area in such case).
3.b. Erase blizzlike data (WDT, WDL, ADTs - everything in world/maps/(your edited map's name)) of your edited maps from blizzlike MPQs.
4. Open patch-3.mpq and in Operations menu choose Change hash table size. Maximize it.
5. Insert whole up-to date version of all blizzlike maps you have edited into patch-3.mpq.
6. Insert all your other custom data you may have into patch-3.mpq. Modified M2s and WMOs, retro-ported models ans so on, any edits which may affect map collisions - so, in general, just everything you have in your custom patches.
7. Run extractors in your extraction-only client.
Like I said, its rather unclean way of doing things, but by following this guide, there is just absolutely nothing what can go wrong. Well, at least not as long as you follow these instrctions correctly.
