UPDATE AND FIXED:
Simply resetting the RTC on PkHex didn't seem to work and was leaving me annoyed with being 2 hours behind suddenly. I went back and started messing around in settings and discovered that the Days Passed in Event Flags>Event Constants was still that over 7800 number from before I reset the clock. In addition I found a previous save backup from before I did the wonder card injections and found the RTC days passed on it was much lower. I ended up changing the RTC times to the exact ones of the old backup and the Event Constant time to match the RTC and when I tried that save it was clear time had passed as my berries had grown. Changing the date on my 3ds 1 day ahead let me do daily events again proving it had fixed it. Also my ingame time matched my 3DS system time again. I'm not sure if it was the lowering of the RTC to the one of my old backup or the matching of the RTC days with the Event Constants that fixed it if anyone comes across this thread in the future but I hope someone may be able to get something from what I've found :))