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I also lost a few of my pay stubs also. The most important piece of document is your reference letter. T4, Noa, and paystubs are used as a check if there are any doubts. I also worked 50 hours a week on several occasions at my last job but my reference letter stated 40 hours a week. Hence, CIC went with 40 hours.
 
Goku said:
Read in thread that some people got rejected because they were short of 1-2 days for completion of 1 year. That's why I want to know how they figure out that they were short of 2 days.

It's fairly simple. Their duration of work was most likely not one year based on reference letter. NO ONE at CIC has the time to verify every single day of an applicant's employment. It would crawl the entire program to a halt in one week.

You should be okay, don't worry about vacation time. It's expected to be part of your employment.
 
Goku said:
Yes Reference letter said I worked 40 hour but I was working around 50 hours a weeks for couple of months. All leave were paid. But how they confirm that all leave were paid or not ?

They would only care if you said you were paid xxxxx for working 40 hours per week, and your T4 showed you earned less than you were supposed to...

Someone who takes 1-2 months of unpaid leave will usually have a gap in their earnings...

From what you've written, I see nothing to worry about.