nope, as soon as you use points on the flight, it becomes ineligible for any FF and status point earn
Velocity Points and Status Credits cannot be earned on:
Reward Seat Bookings Fare classes other than as specified above Any Singapore Airlines flight where KrisFlyer miles have been used as a form of payment irrespective of the fare class flown Codeshare flights (Any flight with an SQ flight number that is operated by an airline other than those operated by Virgin Australia or SilkAir)
I think you'll find that using points to upgrade isn't using miles as a 'form of payment'.
From what I understand you can change the earning account back to VA, but I believe it needs to be done over the phone or at check-in. I can't remember exact details but I'm sure someone will be able to clarify.
I wrote to both SQ and EY with this very question.
SQ were brilliant in their response - the answer is a resounding, uncomplicated "yes". There's no requirement to have flights credited to KrisFlyer if you upgrade using miles.
EY were completely hopeless. The responses went through the following motions (each one in a separate response to asking for clarification):
* Yes, you can earn points with partner programs when flying with Etihad
* Yes, you can upgrade some fares using Etihad Guest Miles
* No, you cannot upgrade codeshare flights with Etihad Guest Miles
* No, you cannot upgrade Etihad flights using Velocity points
* No, you can't transfer miles from Etihad Guest to other programs
* Please call our contact centre - we don't understand the question
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