The only way to mitigate this problem is to upgrade to Word 2016, which does not have this problem. There is a serious bug on Word versions up to and including Word 2013 that causes the first letter of small equations to disappear randomly after some time. Note that Math Builder does not perform any mathematics it is a tool for displaying it.
#WORD EQUATION EDITOR SHORTCUTS 2016 UPDATE#
Note that this is a different tool than the legacy tool Equation Editor 3.0 (which is still available on 32-bit Office versions until the January 2018 update ) and MathType. It also applies to Microsoft PowerPoint and Excel 2010 and higher.
This book is about the Math Builder (officially called as Equation Editor) tool in Microsoft Word and Outlook 2007 and higher.