Should the flag not have been helpful as it pointed out the need for the post to be edited to answer the question?
I'm generally pretty generous when deciding whether to mark flags as helpful or not, but in this case I felt that the better decision (on balance) was to decline. This sends a message that the flag used was incorrect, whereas marking helpful encourages the same usage in future.
The post at that time was, in my judgement, an honest attempt to provide at least a partial answer, which is key to evaluating Not An Answer (NAA) flags. This type of flag should be reserved for contributions that are unambiguously no sort of answer at all.
The second answer (now deleted and edited into the flagged answer) was present at the time your flag was raised. Instead of flagging NAA, you could have made/proposed the edit yourself, and/or flagged one of the answers as 'Other', describing the moderator action required. I would have marked such a flag as helpful for sure.
Alternatively, instead of a flag, a comment could have been left for the answer author (a brand new user at the time) to guide them in site usage and encouraging them to combine/improve their answer(s).
I hope that explains the reason the flag was declined. Your good flagging record is appreciated, and I thank you for asking for clarification via meta.
See also How do I properly use the “Not an Answer” flag? in the SE FAQ.