I tried to recall what I did yesterday, and I think I have found out the reason.
First of all, I have an old version of this set with only 3 diffs in stable. You can it here:
https://kanatama.s-ul.eu/oannnt6c
Then all other diffs except the 3 will disappear after the following steps:
1) enter the Hard diff in stable editor (idk if it has to be the Hard diff)
2) open the beatmap dialog (ctrl+shift+u)
3) when the dialog appears (you are one step away from....), click cancel.
tbh I'm very surprised that the online beatmap is still changed in some way even if it's cancelled before update...
And now when I try to the set from lazer again (on the official build), I get the error "one of the beatmaps to keep does not belong to the specified set".
regarding the questions:
1. I think I accidentally triggered the map update dialog on one map yesterday on stable (and cancelled it), and it looks that this map is the victim
2. it's a long time ago and it has been updated multiple times, so I can't recall, sorry...
3.
https://kanatama.s-ul.eu/oqrmxops
4. usually I map (and submit) with my own build with those tweaks. You can say I have lost the right to ask for help by doing so, but the tweaks should not involve the beatmap submission system and I have used in this way at least since the first day of lazer submission , so I doubt that is the reason