While dbigging PHP code, IDE opens another of the file (with green step debug line) which you can edit, but will loose 
those changes.
This bug is very annoying and misleading. Very easy to reproduce:
- install x-debug
- create some test php file
- start debugging it
  === You will see that Netbeans open another editor instance of this file. This new file instance wouldn't have LOCAL 
HISTORY. 
      If you change that file, changes will be done only on server directory. Thus you will loose changes if update 
sever or restart Netbeans (NB) and edit this file. 
I lost some changes couple times. It wasn't happening with some previous NB version. Please fix ASAP.
Please, let me know if you have any questions.
Regards,
Vlad

You should set break point and start debugging to see that NB opening another instance of the file. Initial file will 
have break point (reg line) and the new instance have just green line highlighting current debugging line.
Regards,
Vlad