Hi there,
I have run into the problem that Jomo and AndrewHF have described repeatedly with my XT3 and MAC O/S. I have had the problem with Big Sur, Mojave and High Sierra (just never had a machine with Catalina) but not Windows O/S. It has something to do with how Fujifilm is formatting the cards. Something to do with too many clusters. (I found this out painfully by using Disk Utility to try to repair the card. Big mistake.) I thought it was only with 128GB cards but it has even happened with my 64 GB. You can lose about 5 GB of data. The pics show up on camera but if you try to download them using an SD card reader on your computer some are missing. For example, on time-lapse shoot that I'm currently downloading, there are pics on one card in folder 102 running from-9658 to -9999 and then folder 103-0001 to 4557, but only up to -4096 shows up on my Mac.
And it's not always the last set of pictures. Depending on where you start the file numbering it could easily occur in the first folder. It's tied to too many files in a folder so you need to be super careful.
I have tried to report this to Fuji but I guess I didn't explain it properly. The solution I have come up with is to first download with SD card reader, because it's so much faster and then re-insert card into camera and use IMAGE Capture software to download the missing files. All Mac computers have this software. Make sure to set up the USB connection on your camera and to connect USB cable to camera and computer before turning on camera. Then start up Image Capture and BE PATIENT!! IF the camera light is flashing, data transfer is occurring. This can take a very long time as will data transfer. I'm fortunate to have an old laptop where I do these downloads so that it doesn't bog down my main machine.
Hope this helps! I'd love if there would be a firmware update to correct this!