I dont actually know the games has limited number of saves, as I usually make 2 to 3 different save, then overwrite among these 2 to 3 saves. You can actually load back to the latest save before this case happen to you.
I saw the message on the loading screen before, but all I can tell you is, I never need to wait for teleporting between my battle tower and real world. I can get in and out now stop, and that how I usually do when gathering raw materials through my runners. Give command to gather, get out of tower, then come in tower again and runner get the job done. And this process usually will be repeat for around 5 to 10 mins to gather tons of raw materials either for crafting or selling for cash.
