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For the record…
Regarding the "deprecated" status of "ais", Amir is almost certainly alluding to the fact that SIL considers the code to be "Deprecated" following this change request (of December 2018). As they explain at their website, such deprecated codes "are no longer in active use, but still have the meaning assigned them when they were established in the Standard."
As to whether "existing translations in 'Sakizaya' made under 'ais' are already in 'Naotoran Amis'", I cannot personally say, but User:StevenJ81 (Langcom member) and User:Corainn (zh-Hant-TW-N user) have discussed this and seem to agree (each from their own perspective) that this is not the case.
In any event, as stated by StevenJ81 in the same discussion, this issue is currently being worked on in phab:T174601. Verdy_p, if you do not agree with the action plan laid out at phab:T174601#5348652, you should comment there.
Edit: StevenJ81 is technically a "clerk" (a non-voting member) of Langcom.
So my comment is still valid: We should have not named "ais" as "Sakizaya" given that "ais" was given the meaning of "Naotoran Amis" in ISO (not SIL which is just the current maintenance RA and does not decide itself!), which is in fact a local dialect of "Amis" but not "Sakizaya" for which ISO assigned a distinct code. ISO also assigne the code "ami" for "Amis" (from which "Naotoran" is a village where both languages "Sakizaya" and "Amis" were used by the two coexisting local communities, and that's why "ais" was named "Naotoran Amis" and not just "Naotoran" which would really have been confusive).
So there was no error in ISO. But the deprecation of "ais" just means that ISO no longer considers it as a distinct language, but as a dialect of "ami", and what occured in ISO was actually not a "code split", but a requalification to cover "Amis" more extensively and "Sakizaya" was never encoded and covered by ISO. So this is another case where an ISO 639-3 code is assigned to a dialect, even if it is not in scope (this can be applied to Maltese [mt] and various other Arabic dialects that also have their own ISO 639-3 code, even if they are normally not in scope of ISO 639-3 which is not supposed to cover dialects, but we also know that the encoding of dialects in ISO 639 was tried and published in a early 1st version, and rapidly abandonned).
We should have never used the name "Sakizaya" in Wikimedia for "ais", as it was wrong since the beginning (even before the ISO change in 2019). It's up to us to not use "Sakizaya" for "ais" and to make it clear that this was an error of Wikimedia (and Translatewiki.net) and not from ISO.