It is not the case.
After I finished the project, the last thing I did to it was
to copy it to another location, and nobody but me has access to
that. I did not delete deliberately the TOC and Index. So, I was
thinking that it happened to somebody else, and therefore I was
asking for an opinion.
As it looks that nobody experienced this till now, I can
offer you my solution to it. I was doing translations to the
original project in English, so I took the original .xpj file from
the English project and copied it with a different name in the
directory of the translated project. I just had to change the
language of the project. Everything else was as they should
have.