RTC not working in Pokemon RSE after moving savegame from GBA

[SaddQ]

The issue at hand is that though I can play my Pokemon RSE perfectly on the EZ Flash Omega on my GBA SP, with working RTC as well (At least on one of my two GBAs), after moving a savegame to my 3DS cias of the same games, suddenly the RTC stops working. No message that the battery has run dry and the in-game clock is still ticking. However, time-based events do not work anymore, so e.g. berries don't grow.
When starting a new game on the 3DS and not moving the savegames, there is NO problem with the RTC whatsoever. Only after moving savegames back and forth to the GBA for the purpose of trading between GBAs (or Colosseum, XD or Pokemon Box) does the clock time in the character's bedroom get messed up and do RTC events stop happening.

Does anyone recognize this issue? Any fix?
I read something about an RTC editor. Could that work?

 

[Raychapa7]

I have the same issue, did you find any solution?

 

[FAST6191]

I don't know specifics offhand or if the omega does some kind of in place hack to change the date format/last opened on format, or tacks on a date to the end of the save and loads that again when it detects a RTC game being loaded, or indeed if the GBA emulator on your 3ds does this. However those would be my first ports of call for something to go wrong here, and indeed starting a new game might have it operate under a different paradigm which would explain the difference.

What to do first involves figuring out what is done but it is not likely to be that difficult -- get various saves (presumably new game first save, and then another/another 2* saves later when the time had advanced a bit) in both and compare it to see what changes, then

*pokemon alternates save slots, how it can do the save corrupted so now loading earlier save thing when you mess something up, hence why saving twice might be the order of the day to get it back to the baseline slot.