FAQ by CIC:
If I have a year of work experience in more than one eligible federal skilled worker job, can I apply more than once?
Yes. You can apply as many times as you like, under the same immigration program or different programs. But, you must pay a separate application fee each time. h
Can I withdraw my federal skilled worker application?
Yes. Contact your local visa office to withdraw your application.
If I withdraw my federal skilled worker application, can I get my money back?
It depends. Your fee will be refunded if the office has not begun processing your application.
About Reference Letter:
Try to get it from supervisor. If not possible, then go with your senior colleague. Ensure adding a cover letter mentioning why reference letter not attained from HR/supervisor and why no cover letter.
Ensure other documents like payslips, joining letter, promotion letter, etc, visiting card of your colleague.