Welcome to the community! Kindly please be informed that this is a know bug and has already been fixed which shall be fixed in the next release (that is taking place very soon). Till then please be sure you do not do the following:
Edit your survey form in the form builder user interface (when you have a matrix question). Doing so will result to what you are currently facing.
Edit and replace the survey project through an xlsform (if you wish to make any edits within your survey project).