It is possible someone may eventually updated the save editor to handle the EE, but since nobody has done so yet, that seems unlikely.
If loading is always at the same state, there must be something preventing the save process from finishing (and overwriting the previous version).
In the profile's savegames_patch folder, try renaming the HonourMode folder and lsv file within (and optionally the png screenshot file). Next, delete the contents of the LevelCache and Temp folders in the My Documents 'Divinity Original Sin Enhanced Edition' folder. After that, start the game, load the save, teleport to a different region and try saving and loading.
If that doesn't fix the problem, exit and delete the 'Divinity Original Sin Enhanced Edition' folder in the Larian Studios My Documents folder (or rename it if you have any saves from another playthrough you want to keep).
Next, start the game, create a new profile when prompted, then exit. Copy latest backup of your honour mode save to the new profile's savegames_patch folder, and then use the
EE pak extractor (latest version
download) to extract the contents of the save (see below), then delete/move the save folder (leaving only the extracted version), start the game, load the uncompressed version, teleport to a different region and see if you can save and load to the new region. As long as you can save I don't see a way after that the game could load to the original location.
After downloading the ExportTool zip, extract it to a folder somewhere appropriate and start the ConverterApp.exe program. Switch to the 'PAK / LSV Tools' tab, in the 'Package path' browse to the 'HonourMode.lsv' file, then for the 'Extraction / source path' browse to that or another profile's savegames_patch folder and enter a new folder for the extracted files (you can copy/paste the path from the path listed above and edit it; ie to be '..\savegames_patch\extracted_save') and click the 'Extract Package' button.