Oh no! I've never seen this happen before. I have the same everdrive cartridge and I haven't seen this issue yet.
1) Do you know your everdrive firmware version? You can get the OS version by pressing select on the everdrive menu and picking device info.
2) Are you using the latest version of the Skyland.gba rom?
3) Would you be able to attach the Skyland.srm file from GBASYS/save/Skyland.srm? If we are using the same cartridge, the same rom, and the same cartridge firmware, then I suppose the save file could be corrupted somehow, and if so I'd like to investigate.