I ran into a strange issue just now attempting to dump my collection of GBA games.
My cart reader is on the latest version of it's firmware at the time of this post, version V2.6 from Jan 18, 2019.
I tried dumping all of the GBA games I have, both the cartridge and save, and then loaded them in an emulator to check that everything was working, and two games had an issue. The first and second Castlevania games for the GBA (Castlevania: Circle of the Moon and Castlevania: Harmony of Dissonance) had an empty save.
I tried plugging the physical carts into my GBA to check, and the save data was gone there too. I was testing Harmony of Dissonance a few minutes before dumping all of them and saw that the save data was still intact, so it wasn't the save battery having died.
I had backed up my GBA collection years ago using a homebrew application on my Nintendo DS to dump a GBA cartridge's ROM and save data to a SD card, so I dug up those old files and attempted to restore my old save from there using this cart reader, and it worked.
I tried testing it and it seems that any attempt to dump either the cartridge's ROM or save erases the save on the cart and dumps a blank save, although it dumps the rom just fine. It also is able to restore the save from a different source just fine too.
I don't have many GBA games, only about a dozen or so, but these seemed to be the only two games effected. I thought maybe it's an issue with GBA games that use SRAM to save, since those games were uncommon, but the third Castlevania game (which I think is SRAM, but not certain) kept it's save when I dumped it, as did other GBA games that use SRAM like Wario Land 4.