Gotcha. Just to make sure I have it right, save a game like normal, then press Home, then exit (rather than saving like normal then just closing the 3DS into sleep mode like I usually do)?
When you close the 3DS or go into sleep mode, sometimes GW bricks. If you don't homeclose before that, you end up crashing out and losing your progress.
Make sense? It's not that sleep mode will kill your game. Just sometimes the system has problems coming back after a long period with GW installed.
So:
Always save game like normal (duh).
Before you close lid and run, HOMECLOSE.
Short periods are okay, but how many times does a "short period" turn into a "uh-oh I forgot to homeclose..." moment.