Hey Neha,
Asking out of curiosity, why do you want to remove .bak file, actually it's a backup file which Mendix needs for it's own usage. Basically this gets used by Mendix when you click on "Revert all changes".
Now if you can explain what exactly you mean by "pull the app". I am assuming you are talking about update you receive file conflict error, can you share the error screenshot with the details for more troubleshooting?
Regards,
Naman Khard