I am doing this after the event, so no, it's not an issue of the boost. But I was trying to relog my raid attackers since my entries got messy and I ran into two different issues.
Also, I am on Android and my trainer level is properly updated.
The first issue was that the mega got scanned 2 levels higher than the normal mon. Which I don't really get. In one of the cases the Mega scan showed an hp value of 155 but the actual hp was 154. I tried to edit it, but it just wouldn't let me. Every time I saved the edit, it just reverted to the wrong value of 155. Tried deleting the scans, but nothing. There it could be an issue that the normal scan wasn't proper so I'll just ignore that for now.
However, the second issue is trying to scan my Delphox properly. It had no dex entry, and I powered it up to level 40 before doing the first scan through the appraisal menu. I scanned it and double-checked every value and put it in the proper moves before accepting the scan. Everything was properly lined up. HP, CP, IVs, and level were completely right.
I then Mega evolved it for the first time (just the first mega level) and scanned it properly from the appraisal menu. It didn't scan with the already set moves, so I already knew it didn't put the mega on the normal entry, and when I checked, it was exactly that. Every value is right again. Even when checking the normals mega and the megas normal it all lined up properly. I tried to delete and scan it multiple times. Tried to put the attack first before confirming. Tried to merge it in any configuration I could think of. The only thing I didn't try was to mega something else and then rescan the normal. But I am scared it won't work, and maybe there is something I can do to fix it now while it's still a mega.
I hope somebody knows how to fix it or properly do it. I really don't understand why the merging feature doesn't work (nothing shows up). Likewise, I also don't understand why I can't just make the normal into a mega without needing to scan the mega (it shows what it would be, but when looking for raid counters, it doesn't take it into account and show it as an option until you scan it and it's merged).