Hi Remko78,
I don't know anything about importing from Word documents, so
can't comment on the TOC problems you are experiencing, but there
are definitely problems with long paths in hyperlinks to other
topics. The hyperlinks work when you view the topic, but don't work
from a compiled CHM.
Try creating a new folder at the top level of your C drive
and copy the project into the new folder. If the TOC is OK in the
new location, the problem must be caused by the long path names.
Anne