I understand your situation and know some pretty awesome workers in the UAE who were still on their spouse's visa.
After moving here, I have observed that Canada is a stickler for the letter of the law, however very lenient when it comes to the human factor. For example, here you will be hit with a major traffic violation no matter what your situation, however go into one of their designated offices and plead guilty and ask for some concession, they won't even give you any black points (your driving record remains clean) and ask you to only pay a nominal fine.
You need to think of this situation from the perspective of Canadian government and their subordinate departments (like CIC). The fact that they have asked for these documents means they have uncovered something in their background checks of your spouse, though there is still a 10% chance they only asked for the work permits as a matter of routine (though this is an unusual requirement).
Assuming CIC background checks have already revealed your wife is in the UAE on a spouse visa, I can think of 2 scenarios that could be going through their minds:
1. They found out that your wife has been working illegally (considering letter of the law and not common practice) on visa that explicitly says she cannot work in that country.
2. They thinks since she cannot legally work in the UAE, the most recent employment letters she has provided are fake and the company has given the letter as the owner might be a family friend.
I would suggest being open and direct about the situation and presenting your case that: a) she did in fact work during this period, b) it is common practice to work like this (more difficult, as you cannot get a letter from the government for this).
From the top of my head I would do the following if I was in your situation (my own opinion):
1. Order your GCMS notes immediately, to understand why you are being asked for the work permits now.
2. Write a cover letter detailing her time on her own visa and then transferring to your visa, with the appropriate reason on why she had to do this.
2a. Do not write convenient timings as a reason for the change of visa, unless you want to build your case on the fact that she was only working part time, as this may effect her points calculation for full-time work experience (other members please comment on this).
3. Attach certified copies of all old labor contracts and cards from the previous jobs.
4. Attach letter from her current company that they are aware she is working on a spousal visa and they have no problem with it.
4a. Have the person signing this letter add his contact numbers at the bottom of the letter and also attach his business card (I hope he does not have the same last name as you or wife
).
Hopefully CIC will not make a big issue out of this, which really depends on what their set precedence of dealing with this matter is (as you have pointed out, your wife is not the only one in UAE doing this and it is not going to be the first time CIC is hearing about this).
But you must also understand that your wife's company is not an authority that can dictate whether or not they can hire someone not authorized to work in the UAE and your strongest case here is that you are not deliberately engaged in trying to break the law. If needed you may also have to plead ignorance, by saying her company said it was OK, so how were you supposed to know? (hopefully it will never come to this).
Best of luck and keep us updated.
Regards,