Files missing after copying to FAT32 USB stick on Mac Mini

Files go missing or appear empty when copying large directory trees to FAT32 on macOS due to FAT32 file-size/volume limitations, macOS metadata handling quirks (like hidden AppleDouble .DS_Store or resource-fork files), or cluster/allocation table corruption on large drives formatted as FAT32.

Importantly, individual files larger than 4GB cannot be stored on a FAT32 file system at all.

More info from Apple: File system formats available in Disk Utility on Mac

Why This Happens

• 4GB Single File Limit: Any individual file larger than 4GB in your 93Gb folder will fail to write or cause silent/truncated errors on FAT32. 
• macOS + FAT32 Poor Compatibility: Apple’s native implementation of FAT32 and ExFAT can mismanage directory tables, leading to ghost storage usage (space marked as taken) or folders appearing empty.
• Hidden/Metadata Files: macOS writes hidden resource files (._filename) to non-native file systems, which can clutter or break FAT32 root and subfolder indexing.

How to Fix It & Copy Your Files Properly

Reformat the USB Stick to ExFAT or APFS/Mac OS Extended:

• FAT32 is outdated and ill-suited for a 256GB drive containing 93GB of data.
• Open Disk Utility on your Mac.
• Select your USB stick in the sidebar (make sure you select the top-level drive, not just the volume).
• Click Erase and choose:
  • ExFAT if you need to use the USB stick on both Mac and Windows.
  • Mac OS Extended (Journaled) or APFS if you are only using it on Macs.
  • Try copying your folder again.

More info: Disk Utility User Guide for Mac - Apple Support

Check for Individual Files Over 4GB:

• If you must use FAT32, check if any single file inside your 93GB folder exceeds 4GB. If it does, FAT32 will reject or corrupt it. You will need to compress/split the archive or use ExFAT.

There are bogus flash drives which will do this; devices that claim to contain more storage than they actually do.

Try a different flash drive from a different vendor.

If you’re inclined to investigate the possibility lf counterfeit or fake flash, and if source code isn’t all that scary, f3.

There are also corruptions within FAT too, as FAT is not a particularly robust file format. This both corruptions, and implementation disagreement around how FAT actually works, the latter due to Microsoft being short-sighted about their business practices.

That aside, where are these files going? To another Windows PC on the local network? If so, set up an SMB file server on one or the other. There are also cross-platform browser-based AirDrop analogs available.

nexial-probe wrote:

Yes - I'm wondering if this is the case - I very much doubt these are genuine Lenovo devices.

Even if they are Lenovo USB sticks, they are most likely junk anyway. If Lenovo provided a USB stick to a user, then that USB stick is most likely going to be cheap. The quality of most USB sticks are junk.....even from some "respected" brands. In my own experience, SanDisk tends to be the most reliable....I've even had good luck with the MicroCenter branded USB sticks.

If you are going to be transferring that much data at one time, then you should invest in a slightly higher end USB stick which at the very least supports 150MB/s write speeds (or even 100MB/s). I know SanDisk makes a few USB sticks like this, but it can be very hard to figure out which ones they are. You have to read the product documentation & data sheets very carefully to find this information. If you cannot locate this information, then assume the write speeds are embarrassingly abysmal 10MB/s.

I'll try using my Linux box to write the USB. It just means I have to copy Gb and Gg of stuff to it from my Mac.

I don't like to copy large amounts of data using the Finder. I would suggest using an app like Carbon Copy Cloner (CCC) to transfer large amounts of data (I already paid for it for other reasons). I like it because it will log any items which cannot be transferred. Or I may use the command line to perform the transfers. I don't find the Finder very reliable on large transfers.

nexial-probe wrote:

The format must be FAT32 or it can't be read by the device I'm plugging it into in the end. None of the files are over 500Mb - the vast majority are around 60 to 100Mb.

Have you tried to re-format the USB stick on the Mac? You might also try if for some reason MS-DOS (FAT) and MBR (Master Boot Record) works better than GUID partition scheme. If not, maybe that USB stick is bad.

p.s. After copying files to the USB stick, you might want to delete the '._' dot files that carry some Mac-specific extended file attributes that Windows/Linux do not understand (and are usually not needed anyway):

Copy and paste (without [folder path]) the following command to the Terminal window and type a space to the end, and drag the USB drive to the end, and press Return. Then eject the USB drive without opening it in the Finder (so new dot files are not generated).

dot_clean -mn [folder path]

Yes - I'm wondering if this is the case - I very much doubt these are genuine Lenovo devices.

I realise the limitations and pitfalls of FAT - believe me I'd rather not use FAT - but I'm stuck with various other factors I have to work around.

I'll try using my Linux box to write the USB. It just means I have to copy Gb and Gg of stuff to it from my Mac.

nexial-probe wrote:

I've been using Macs since 1985 (I sh¡t you not) and I've never found the finder to be that unreliable. "Drag, drop, go to long lazy lunch" has always worked.

It's not 1985 anymore. I can assure you the Finder is unreliable.

It's certainly possible that the USB sticks are bad. However, modern macOS is, what's the word I'm looking for...junk! Yeah, that's it.

A couple of years ago, Apple re-wrote the MS-DOS-style device drivers using FSKit, a new "user-space" file system driver. It's junk. Even before recent AI-fueled madness, macOS has struggled with foreign file systems. What you describe seems very similar to what I used to see back in macOS 10.9 days trying to get WebDAV servers to work. The more folders and subfolders you add, the worse the reliability.

You haven't gone into a lot of detail about how you're debugging this problem. Did you try taking the stick out and putting it back in? Maybe after restarting the Mac? You said you have a Linux machine. Did you try the written stick on that to see if the data is there.

You've checked the total size, and it seems to have allocated space. Sometimes Apple likes to write files into hidden directories and later move them into place and/or rename folders. So look for hidden folders that might not correspond to your desired hierarchy.

The format must be FAT32 or it can't be read by the device I'm plugging it into in the end. None of the files are over 500Mb - the vast majority are around 60 to 100Mb.

The very first folder copied (seems to choose one at random) is ok and comes across with all its files and subfolders intact. Every other folder is empty, despite Get Info showing the drive now has 93Gb used up and the operation taking a couple of hours.

Thanks. I'll take a look at CCC. I've been using Macs since 1985 (I sh¡t you not) and I've never found the finder to be that unreliable. "Drag, drop, go to long lazy lunch" has always worked.

Sadly I have no control over which USB sticks I'm using for this project - there are many many things I'd do differently if I could.