It appears the level cache file for Luculla Forest and the mines, at least, got carried into your second playthrough.
The safest way to proceed would be to revert to a save before entering Luculla Forest for the first time, delete the file(s) that were added early and continue from there. Deleting the files in your most recent save would get the game to replace them with the default versions, as well, but that could cause problems in quests you have started, result in missing or duplicate items, and reset opponents, etc.
You can email supportdos@larian.com with your last Cyseal save, or I will describe how to fix it yourself, if you wish.
Saves can be opened in the
EE pak extractor program: (
download).
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.
Now browse to that extracted path in Windows Explorer, and in the levelcache folder delete or move the files for any areas you have not already cleared (lucullaforest.lsf and luc_mines.lsf at least: darkforest = Phantom Forest, theprisongardenofstoneking = Hiberheim and the rest should be obvious).
After that, you can just start the game and load the extracted save; the game will see the extracted folder as a save, so you don't need to worry about packing it.