topic links switch to project path links and break

Robohelp 11

Some links that worked yesterday switched to the complete path name and are broken today because they're outside the project. For example: <a href="ma_stu_roster.htm"> became <a href="git/helpfile/projectname/ma_stu_roster.htm".

Yesterday I did a find/replace for a word, which would change text on the HTML tab. However, if this is the problem, there should be many more broken links, as the replaced word was common. I know there can be a problem editing the HTML tab directly. What's happening and how can it be done to avoid breaks? 

Thank you