Most likely the level files for the Black Cove and homestead were carried into the new game from the main level cache folder. Extracting the contents of the save file and deleting/moving the files for those regions would allow the game to load the default versions, which would hopefully avoid any issues up to that point (since with an honour mode save you wouldn't have the option of reloading an earlier save, before first entering); just resetting the file after already exploring part of an area could cause problems with resetting opponents, duplicate items, etc.
This can be done with the EE pak extractor (download), if you still have a copy of your save. After starting the ConverterApp.exe program, switch to the 'PAK / LSV Tools' tab, in the 'Extract Package' section, for the 'Package path' browse to the save's lsv file, then for the 'Destination 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\SaveName-extracted') and click the 'Extract Package' button. After renaming or deleting the cys_blackcove.lsf and homestead.lsf files from the levelcache folder (and any others from later regions), you can load the extracted save, and hopefully continue from there.
