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I'm not sure I'm following this..."new ETA" and "new VISA stamped". Just take a copy of the new eVISA and they'll put the eVISA entry in your passport.
I don't think it is complicated.
 
An ETA is not a VISA but just an Electronic Travel Authorization. Having an ETA doesn't mean that the VISA is entirely approved (i.e., immigration officials can still reject at entry but this doesn't happen often). Only VISAs stamped on your passport is a valid VISA.

Having said that, the first half of my question was more about the chances of getting a new ETA approved while the current one hasn't expired. I've read online that there is a good chance that it might get rejected and I'll need apply only after the current VISA's expiry. The 5 yr e-VISA seems to have a high success rate in similar scenarios but unfortunately, India doesn't provide 5-yr e-VISA to Canadians.