I assume that you're working in Word - is this correct?
May I suggest to search this forum for "hidden text" - in fact, the issue has been discussed numerous times.
But last week something happened to my bilingual files. Basically, everytime I close a translation segment, the source language is not there anymore, it looks as if the document was already cleaned up. Of course, I can still open every segment, but it is quite frustrating as I can´t see the 2 languages anymore. Also, one of my customers asked (for the first time, Murphy's law) to provide them with the bilingual file and the cleaned up one...and I don´t know what to do to solve this issue...
The display of hidden text does not affect the presence of source segments - what you will need to do is to clean up the file. I suggest to look at the Trados File Formats Reference Guide for a workflow description.