Hi,
I have been modifying the FPJ files for a long time now, in
both X5 and RoboHelp 7. It is true that the folder fpj file is what
keeps track of the topics in the folder. When I get an issue with a
red X through a topic, I know that it is because there is no entry
in the fpj file for that topic. I check out the fpj file, create an
entry for that topic, and then I check it back in. It always fixes
my problem. However, this is an XML file, and not everyone is
comfortable editing this file probably. I'm not positive why your
issue happened after your upgrade. To answer your question 1, you
are getting that message bcause the fpj file in your local projects
is different than the one that is in the database. Usually, it is
caused by someone deleting, adding, or renaming a topic htm
filename and source control not getting it updated correctly. That
can be due to a connection issue or other error and can be hard to
pinpoint what caused it exactly.
On your question 2, it may be okay to replace it. If you try
the replace and then have some issues with topics in that folder,
you can try fixing it yourself by checking out the fpj, modifying
it to contain the correct topics, and then checking it back in. In
the fpj file, it's actually pretty easy to make copies of the
entries and then just change the htm filename, or delete entries of
topics that no longer exist.