Hi,
IMO, you will get a TRV if you present your paperwork properly. You have good, strong ties.
Visa officers don't have too much time to go through passports and figure out entry/exit stamps or the latest residence permit. That's why good paperwork makes the difference.
When you reapply, do include a cover letter with separate sections for:
Applicant details + Refusal reasons and addressing them + Immigration status in the UAE (scan the resident permit + state details) + Strong ties to the UAE + Strong ties to India + Purpose of Visit (itineraries + credentials of the tour company) + Available funds for my visit + Financial situation + Travel History (chronological in a tabular format + scan UK, Australia and Schengen visas) + Why I must return to the UAE by XX date.
Do highlight the Unlimited Work Contract.
No long, run on sentences. Keep it short with facts in point format + give reference numbers to evidence/cross references to evidence in the cover letter.
Include detailed expense estimates to prove you can afford the visit.
Also include an overseas travel medical insurance policy to match your intended visit dates + 2-3 months' credit card statements (state you will bring these CCs)
Do highlight the bank transfers from your UAE bank account to the India one. You obviously cannot be physically in two places at the same time. So you can explain that your parents withdraw these funds from the ATM.
Also include evidence, for example: You pay rent for their place, utility bills, medical insurance, etc
Do include the property documents which I had suggested. Affidavits/CA valuations won't work in isolation. Supporting evidence is essential.
I suggest you include the additional documents I had mentioned.
Unfortunately, tour companies don't take responsibility for visa refusals.... nor do they have the unenviable task of declaring visa refusals for any future visa applications.
Here's how to order:
http://www.cic.gc.ca/english/department/atip/requests-atip.asp
No, GCMS notes will not affect your future applications. It helps to understand why you were refused.
Fingers crossed your wife gets her TRV soon