Hello again
Let me ask. When you edit the topics that give the headaches,
do you see little red squares in them?
Here's the deal. When you instruct RoboHelp to generate your
output, it dutifully copies each topic file into memory. Based on
the settings in the Single Source Layout, it injects different
JavaScript codes into the topic. The modified topic is then saved
in the !SSL!\WebHelp folder. (or !SSL!\FlashHelp if that's your
flavor).
There are a variety of ways that output files may overwrite
source files. The most common way is by the help author unwittingly
defining the source location as a Publishing Destination. But there
are other ways it can happen too.
Do you have Publishing configured? If so, perhaps examine
that process.
Cheers... Rick