File actually on the site -->
http://www.conquerclub.com/maps/Waterloo.xml[spoiler=File 1 details]<territory>
<name>Ney 03</name>
<borders>
<border>Ney 02</border>
<border>Ney 04</border>
<border>la Haye Sainte 01</border>
<border>Ney 01</border>
<border>Alton 05</border>
<border>Ney 05</border>
<border>Ney 06</border>
<border>Alton 03</border>
<border>Alton 04</border>
<border>Alton 01</border>
<border>Alton 02</border>
</borders>
<coordinates>
<smallx>261</smallx>
<smally>362</smally>
<largex>349</largex>
<largey>475</largey>
</coordinates>
</territory>
<territory>
<name>Ney 05</name>
<borders>
<border>Ney 03</border>
<border>Ney 04</border>
<border>Ney 06</border>
<border>Alton 01</border>
<border>Alton 02</border>
<border>Alton 03</border>
<border>Alton 04</border>
<border>Ney 02</border>
<border>la Haye Sainte 01</border>
<border>Clinton 09</border>
<border>Imperial Guard 08</border>
<border>Clinton 02</border>
<border>Clinton 03</border>
<border>Clinton 04</border>
<border>Clinton 05</border>
<border>Uxbridge 01</border>
<border>Alton 05</border>
</borders>
<coordinates>
<smallx>261</smallx>
<smally>313</smally>
<largex>349</largex>
<largey>409</largey>
</coordinates>
</territory>
<territory>
<name>Ney 04</name>
<borders>
<border>Ney 05</border>
<border>Alton 03</border>
<border>Alton 01</border>
<border>Clinton 09</border>
<border>Imperial Guard 08</border>
<border>Ney 03</border>
<border>Ney 06</border>
<border>Alton 02</border>
<border>Alton 04</border>
<border>Imperial Guard 07</border>
<border>Clinton 08</border>
<border>Clinton 02</border>
<border>Clinton 03</border>
<border>Reille 06</border>
<border>Hougomont 02</border>
</borders>
<coordinates>
<smallx>230</smallx>
<smally>296</smally>
<largex>308</largex>
<largey>386</largey>
</coordinates>
</territory>[/spoiler]
File you posted -->
download/file.php?id=1630[spoiler=File 2 Details]<territory>
<name>Ney 03</name>
<borders>
<border>Ney 02</border>
<border>Ney 04</border>
<border>la Haye Sainte 01</border>
<border>Ney 01</border>
<border>Alton 05</border>
<border>Ney 05</border>
<border>Ney 06</border>
<border>Alton 03</border>
<border>Alton 04</border>
<border>Alton 01</border>
<border>Alton 02</border>
</borders>
<coordinates>
<smallx>261</smallx>
<smally>362</smally>
<largex>347</largex>
<largey>474</largey>
</coordinates>
</territory>
<territory>
<name>Ney 04</name>
<borders>
<border>Ney 05</border>
<border>Alton 03</border>
<border>Alton 01</border>
<border>Clinton 09</border>
<border>Imperial Guard 08</border>
<border>Ney 03</border>
<border>Ney 06</border>
<border>Alton 02</border>
<border>Alton 04</border>
<border>Imperial Guard 07</border>
<border>Clinton 08</border>
<border>Clinton 02</border>
<border>Clinton 03</border>
<border>Reille 06</border>
<border>Hougomont 02</border>
</borders>
<coordinates>
<smallx>230</smallx>
<smally>295</smally>
<largex>309</largex>
<largey>386</largey>
</coordinates>
</territory>
<territory>
<name>Ney 05</name>
<borders>
<border>Ney 03</border>
<border>Ney 04</border>
<border>Ney 06</border>
<border>Alton 01</border>
<border>Alton 02</border>
<border>Alton 03</border>
<border>Alton 04</border>
<border>Ney 02</border>
<border>la Haye Sainte 01</border>
<border>Clinton 09</border>
<border>Imperial Guard 08</border>
<border>Clinton 02</border>
<border>Clinton 03</border>
<border>Clinton 04</border>
<border>Clinton 05</border>
<border>Uxbridge 01</border>
<border>Alton 05</border>
</borders>
<coordinates>
<smallx>261</smallx>
<smally>313</smally>
<largex>351</largex>
<largey>406</largey>
</coordinates>
</territory>
<territory>[/spoiler]
If you see, Ney 04 and Ney 05 aren't listed in the same order.
In the first file, it is ney 03, ney 05, ney 04
In the second file it is ney 03, ney 04, ney 05
The game stored the territories with a " number" , so for example ney 04 could be the 10th territory. If you change its position, making it the 9th region, when the game will read the file, it will search for the 10th territory, not for ney04, so the game will mess up because de facto ney 05 will be ney 04 with your new file. So, if before the update you had ney04,after it you'll find yourself with ney05.
The same is for continents. You can change all names, coords, features, but you must keep the same order of the current live file when you list them

In few words what i'm asking you is to swap ney 04 and ney 05 positions in your new xml to have them as they are in the current one that's live. Don't worry, no one will notice they are not in order in the xml because the drop down list will be a-z anyway so there's no difference while playing.