Allow me to rephrase your explanation.X means that you are not a real applicant. it is a trick to cover their delay and when the processing will start they will remove it from E.
Application numbers usually have 1 letter and 9 numbers. For example:
Citizenship: C123456789
Work permit: W993830598
Economic class: E099977028
Sometimes IRCC issues temporary file numbers. Therefore, you see an X at the beginning of the application number. However, if they proceed with the application, they will remove the X. On rare occasions, they could replace the temporary file number with a completely new one.