The system clock, used by many softwares, needs to be set to the current date and time to function properly. There are 2 methods for setting the clock. Method 2 is recommended, however there isn't one that works "more."
Setting the clock via System Settings is pretty straightforward.
Setting the clock via GodMode9 is different. It is significantly harder to get screenshots for this, and the pictures weren't very good, so it'll just be text.
Shut your 3DS down. (Hold the power button for about 5 seconds and wait for the lights to fade.)
Hold Start and Power simultaneously to boot the system into GM9. There should be a huge logo that says GodMode9, and then it will transition into a different screen.
At this point, two things may happen:
If it shows up saying the time and date may be wrong, you do not need to navigate further, from there you can set the time, and reboot the system by pressing start. This is most likely because you removed the battery.
If it loads into a menu, press HOME. There should be a popup menu that reads: HOME button pressed. Select action:. From here, you would want to select More..., at the bottom of the menu. In the More... menu, you would scroll down to Set RTC date&time. Once selected, press A. From there, you can set the time and press Start. Press A to close the text and press Start again to reboot the system.
You would most likely need to go to System Settings and fix the date.