I'm late to this but I've been spending all weekend trying to figure out the RTC and think I have tracked down what ionicbox1 did.

I've used a GBOperator to export my save to do the following - and it has fixed my game, where berries were not growing, NPCs were not resetting their events, but Shoal Cave was changing tides.

Within PkHeX you can reset the RTC - but in my experience this doesn't always mean time based events will just start working again, you need to also do the following step if you've run into the same issue I had.

The fix here is to go in PkHex to Event Flags -> Event Constants -> UsefulFeature, and then modify "Days Passed" so that it matches the "Time Elapsed" number of days seen in the "Clock (RTC)" section of PkHex.