By the end of Negima, whenever Negi sneezed he went Super Saiyan 3 and he blew the clothes of everyone around him. That later part is something that still holds by the end of UQ Holder as a weekly. Plus, in the chapter near the end where Konoka was overjoyed to see Asuna again and Setsuna tried to act like Asuna’s servant, it was stated they didn’t see her or Negi so much around anymore, since they were busy with the preparations.
The UQ Flashback has Negi’s sneeze only lifting the girls’ skirts up, his hair doesn’t change, and Asuna is obviously at Mahora as a student. So it should take place before the trip to Mundus Magicus. Since Asuna seems very friendly towards Negi, it’s probably post Mahorafest, when she wasn’t so much of a Tsundere to him anymore.
So my best guess is, after Chao’s defeat but before Magical World. Then again, Akamatsu’s writing is so full of holes and contradictions by now anything might go. Maybe he can just cover himself with the ‘alternate timeline!’ excuse.
“or maybe it is planned to be this way and just a continuation of Negima.”
Seems doubtful. The initial promo cast show seemed to indicate a lot of focus on all new rather than returning characters (almost half of which haven’t been properly introduced more than 100 chapters in– imagine if Rakan had been in the Chapter 1 spread image of Negima). I think there was a major change of plans regarding focus and direction along the way.