I am experiencing similar issues. From this post (see last reply): Unable to remove/delete object from the object repository. it turns out it was due to a corrupt Object file. You may have to find out if the XML structure of any of your object files has been corrupted in a similar fashion. My issue wasn’t due to a Git merge text appearing in the object file, instead one of my object files had text like this:
//<![CDATA[
//]]>
However, I am experiencing issues where the pathways to my objects in my test cases do not update when they are moved. I seriously would like a developer to shine some light on this issue.