I have an EZ Omega flash cart, haven't used it in ages, but from memory, the internal battery inside the flash cart is used for Real Time Clock (RTC) only, not used for game saves.
Just make sure your SD CARD is formatted correctly:
- SD CARD under 2gb, format to FAT/FAT16 32kb cluster.
- SD CARD between 2gb and 32gb, format to FAT32 32kb cluster.
- SD CARD between 32gb and 128gb, format to exFAT 32kb cluster or later.
As JaapDaniels advised, try updating the firmware, download should be at the EZ Flash website.