As far as I have tested this: And I have downgraded my own, and four other N3DS systems personally myself:
9.5-9.7 maybe are unstable. I did initial downgrade attempts on two brand new from a box N3DS systems and both failed at certain point of the downgrade, as did a used system that still was on older firmware, around 9.6-9.8 range but do not recall exactly.
9.9 has seemed to be stable... enough. On O3DS systems I had no problem and personally I downgraded a 9.9 N3DS XL FINE with SafeSysUpdater.
Here is some ground things about N3DS downgrading:
The exploit is very, VERY finnicky. On N3DS systems the race rarely wins. It is adeal where you keep trying the safe sysupdater until it just works. I had to personally do ~100 tried over 5 hours for my own system. A friend I assisted for downgrading on his N3DS XL over chat was making attempts for three days and giving up after hour or so until on day 3 SafeSysUpdater HAX succeeded on first try.
It MATTERS what payload you use. If you are NOT using menuhax, USE MENUHAX. I am not even joking I once on O3DS which is FAR MORE likely to almost ALWAYS succeed with the memchunk2 hax, failed three times in a row when using other payloads until I realized maybe Menuhax does make a difference; and it did.
What you are describing is basic race attack failures that you will see, and could possibly see tens more before the one time it succeeds, and frankly the one time it needs to succeed.
I do not know how you found out about downgrade process but just missed the whole memo about it probably working with 5/100 change, by average on N3DS systems. You just hit your head against it until it works. We will not help more if you fail to understand:
pink dots in SafeSysUpdater = HAX failed. You will see this just as much on 10.3 both 9.9 and 10.3 will fail and fail until it eventually succeeds.
Same thing for SysUpdater but on 9.9 I would recommend to stick to SafeSysUpdater. Really.
rolling?
] On Guard 
