So yay! I reset my cycling town. The starting villagers had a dreamie- Pekoe! I cycle and she's first up! ok! I save after being told she's in boxes Aug 13th 10 am (my irl time was 10 om). I no longer TT in my main town (or as much) so I waited til Drake moved out this morning. I pop my cycle town into my husband's DS and don't pay attention to the date. It loads up and she's gone. Date is now 10/13 what! I didn't touch the date. My husband also disapproves of TT so he would never have messed with his DS clock. I quit without saving uselessly jic. Pop my cycle town into my own DS and date is magically back to August 13th without me changing it but damage is done and Pekoe gone (off to the trading plaza I go lol). What happened?! I checked husband's game (he has a digital copy) and it was at the current irl date because again he never TTs. My own main town is at current date. idk some kind of crazy random error? This is the 2nd time I've lost Pekoe to voiding- the first time the cycler accidentally did it when I was buying her from the plaza lol. Lesson learned; Always check the date. I wouldn't have touched the month because it's a new town and I was going day by day til someone was in boxes which ofc first up was the villager I wanted bah! I might buy a 2nd 3ds just to avoid switching cartridges out- Idk.
Oh I'm so sorry, that sucks. I can't help with the cycling aspects at all, but I highly recommend one 3ds/2ds per game. I've never had a random glitch like you described hapoen though I've changed my own date all kinds of ways I didn't intend to. I'll be more watchful of my date in the future in case that happens to me.