It seems that this affects only devices that write FIT file protocol version 1.0 as those files are converted to version 2.0 for the API. Devices writing v2.0 natively seem to be not affected. But that may change.
Based on their response, this seems like an intended change. They say "All messages and fields previously documented in the FIT SDK are still available. Undocumented messages and fields are being removed before files are sent to third-party platforms." - and yes, they are right: Those fields have been undocumented and have never been 'official' or stated as reliable.
And always remember: The VO2max estimate by file is not an estimate for the single activity, it's simply the user's current estimate. It is (or was) part of the undocumented users profile message.
I, personally, do not like this decision, and it's not my job to rate if from business perspective it's a smart move. But I think there's nothing Garmin users can do about it (besides complaining).