I recently took over a large RH project and discovered that 600 of the 800 topic files in the source folder are actually webhelp files. I checked backups going back over a year, and found that the webhelp is in the backups as well. And yes, the topics do display red boxes at the top and bottom in Robohelp HTML.
I've seen the RoboWizard instructions for cleaning up this situation, but those instructions were written in 2004. I’m wondering if there’s a newer or easier way to clean the scripts and other extraneous coding from the topic files.