Since you are using Wine, you can actually create a new Documents folder in the wineprefix for BYOND. This way it won't affect your Linux "Documents" where you have personal data.
All Wine does is create a symbolic link to "Documents"
Delete the symbolic link here:
/home/username/.PlayOnLinux/wineprefix/byond/drive_c/users/username/
Then just create a new folder, name it Documents.
Then go back to your Linux Documents and copy any game files related to BYOND to the new Documents folder you created. It should run fine now!
Edited by booman